#.......# 
 S.......S 
  T.....E 
    R.Q 
     U 
    E.C 
  N.....T 
 C.......U 
 #.......R
  E.....E 
    S.S 
    

Structures and Sequences

3D structures of components of restriction-modification systems and related proteins


Source of the list: REBASE, last update: 01/28/2015

NPIDB is database of structures of protein - nucleic acids complexes, see reference. NPIDB provides various tools to analyze complexes.

Enzyme ID and link to REBASE Enzyme PDB code NPIDB entry (link)
C.BclI Control protein 2B5A
C.Csp231I Control protein 4JQD yes
C.Csp231I Control protein 4JCY yes
C.Csp231I Control protein 4JCX yes
C.Csp231I Control protein 3LIS
C.Csp231I Control protein 3LFP
C.EcoT38I Control protein 2EF8
C.Esp1396I Control protein 4IVZ yes
C.Esp1396I Control protein 4IA8
C.Esp1396I Control protein 4I6U
C.Esp1396I Control protein 4I6T
C.Esp1396I Control protein 4I6R
C.Esp1396I Control protein 4I8T yes
C.Esp1396I Control protein 4IWR yes
C.Esp1396I Control protein 4FN3
C.Esp1396I Control protein 4F8D
C.Esp1396I Control protein 4FBI
C.Esp1396I Control protein 3UFD yes
C.Esp1396I Control protein 3S8Q yes
C.Esp1396I Control protein 3FYA
C.Esp1396I Control protein 3G5G
C.Esp1396I Control protein 3CLC yes
H-DreI Homing endonuclease 1MOW yes
I-AniI Homing endonuclease 1P8K yes
I-Bth0305I Homing endonuclease 3R3P
I-CeuI Homing endonuclease 2EX5 yes
I-CreI Homing endonuclease 4AQX yes
I-CreI Homing endonuclease 4AQU yes
I-CreI Homing endonuclease 4AAB yes
I-CreI Homing endonuclease 4AAD yes
I-CreI Homing endonuclease 4AAE yes
I-CreI Homing endonuclease 4AAF yes
I-CreI Homing endonuclease 4AAG yes
I-CreI Homing endonuclease 2VBJ yes
I-CreI Homing endonuclease 2VBL yes
I-CreI Homing endonuclease 2VBN yes
I-CreI Homing endonuclease 2VBO yes
I-CreI Homing endonuclease 2O7M
I-CreI Homing endonuclease 2I3P yes
I-CreI Homing endonuclease 2I3Q yes
I-CreI Homing endonuclease 1U0C yes
I-CreI Homing endonuclease 1U0D yes
I-CreI Homing endonuclease 1T9I yes
I-CreI Homing endonuclease 1T9J yes
I-CreI Homing endonuclease 1N3E yes
I-CreI Homing endonuclease 1N3F yes
I-CreI Homing endonuclease 1G9Y yes
I-CreI Homing endonuclease 1G9Z yes
I-CreI Homing endonuclease 1BP7 yes
I-CreI Homing endonuclease 1AF5
I-DmoI Homing endonuclease 2VS7 yes
I-DmoI Homing endonuclease 2VS8 yes
I-DmoI Homing endonuclease 1B24
I-HjeMI Homing endonuclease 3UVF yes
I-HmuI Homing endonuclease 1U3E yes
I-LtrI Homing endonuclease 3R7P yes
I-LtrWI Homing endonuclease 4LQ0 yes
I-MsoI Homing endonuclease 2FLD yes
I-MsoI Homing endonuclease 1M5X yes
I-OnuI Homing endonuclease 3QQY yes
I-PpoI Homing endonuclease 2O6M yes
I-PpoI Homing endonuclease 1EVW yes
I-PpoI Homing endonuclease 1EVX
I-PpoI Homing endonuclease 1CYQ yes
I-PpoI Homing endonuclease 1CZ0 yes
I-PpoI Homing endonuclease 1A73 yes
I-PpoI Homing endonuclease 1A74 yes
I-PpoI Homing endonuclease 1IPP yes
I-SceI Homing endonuclease 3C0W yes
I-SceI Homing endonuclease 3C0X yes
I-SceI Homing endonuclease 1R7M yes
I-Ssp6803I Homing endonuclease 2OST yes
I-TevI Homing endonuclease 1T2T yes
I-TevI Homing endonuclease 1MK0
I-TevI Homing endonuclease 1LN0
I-TevI Homing endonuclease 1I3J yes
I-Tsp061I Homing endonuclease 2DCH
I-Vdi141I Homing endonuclease 3E54 yes
PI-PfuI Homing endonuclease 1DQ3
PI-PkoII Homing endonuclease 2CW7
PI-PkoII Homing endonuclease 2CW8
PI-SceI Homing endonuclease 1UM2
PI-SceI Homing endonuclease 1LWS yes
PI-SceI Homing endonuclease 1LWT yes
PI-SceI Homing endonuclease 1GPP
PI-SceI Homing endonuclease 1JVA
PI-SceI Homing endonuclease 1EF0
PI-SceI Homing endonuclease 1DFA
PI-SceI Homing endonuclease 1VDE
BpuSI DNA methyltransferase 3S1S
M.BthVORF4518P DNA methyltransferase 2OKC
M.EcoKDam DNA methyltransferase 4GOO
M.EcoKDam DNA methyltransferase 4GON
M.EcoKDam DNA methyltransferase 4GOM
M.EcoKDam DNA methyltransferase 4GOL
M.EcoKDam DNA methyltransferase 4GBE
M.EcoKDam DNA methyltransferase 2ORE
M.EcoKDam DNA methyltransferase 2G1P yes
M.EcoKI DNA methyltransferase 2Y7C
M.EcoKI DNA methyltransferase 2Y7H yes
M.EcoKI DNA methyltransferase 2AR0
M.EcoKO157ORF1953P DNA methyltransferase 3G7U
M.EcoT4Dam DNA methyltransferase 1YFL yes
M.EcoT4Dam DNA methyltransferase 1YFJ yes
M.EcoT4Dam DNA methyltransferase 1YF3 yes
M.EcoT4Dam DNA methyltransferase 1Q0S
M.EcoT4Dam DNA methyltransferase 1Q0T yes
M.HaeIII DNA methyltransferase 3UBT yes
M.HaeIII DNA methyltransferase 1DCT yes
M.HhaI DNA methyltransferase 2ZCJ yes
M.HhaI DNA methyltransferase 2Z6U yes
M.HhaI DNA methyltransferase 2Z6Q yes
M.HhaI DNA methyltransferase 2Z6A yes
M.HhaI DNA methyltransferase 2UZ4 yes
M.HhaI DNA methyltransferase 2UYH yes
M.HhaI DNA methyltransferase 2UYC yes
M.HhaI DNA methyltransferase 2I9K yes
M.HhaI DNA methyltransferase 2HR1 yes
M.HhaI DNA methyltransferase 2C7P yes
M.HhaI DNA methyltransferase 2C7Q yes
M.HhaI DNA methyltransferase 2C7R yes
M.HhaI DNA methyltransferase 2C7O yes
M.HhaI DNA methyltransferase 1SVU
M.HhaI DNA methyltransferase 1SKM yes
M.HhaI DNA methyltransferase 1M0E yes
M.HhaI DNA methyltransferase 1FJX yes
M.HhaI DNA methyltransferase 2HMY
M.HhaI DNA methyltransferase 10MH yes
M.HhaI DNA methyltransferase 9MHT yes
M.HhaI DNA methyltransferase 8MHT yes
M.HhaI DNA methyltransferase 6MHT yes
M.HhaI DNA methyltransferase 7MHT yes
M.HhaI DNA methyltransferase 5MHT yes
M.HhaI DNA methyltransferase 3MHT yes
M.HhaI DNA methyltransferase 4MHT yes
M.HhaI DNA methyltransferase 1MHT yes
M.HhaI DNA methyltransferase 1HMY
M.HsaDnmt1A DNA methyltransferase 3PTA yes
M.HsaDnmt1A DNA methyltransferase 3EPZ
M.HsaDnmt1B DNA methyltransferase 3SWR
M.HsaDnmt3A DNA methyltransferase 3LLR
M.HsaDnmt3A DNA methyltransferase 3A1A
M.HsaDnmt3A DNA methyltransferase 3A1B
M.HsaDnmt3A DNA methyltransferase 2QRV
M.HsaDnmt3B DNA methyltransferase 3QKJ
M.HsaDnmt3B DNA methyltransferase 3FLG
M.HsaDnmt3L DNA methyltransferase 2QRV
M.HsaDnmt3L DNA methyltransferase 2PV0
M.HsaDnmt3L DNA methyltransferase 2PVC
M.MmaGORF429P DNA methyltransferase 3KHK
M.MmuDnmt1 DNA methyltransferase 4DA4 yes
M.MmuDnmt1 DNA methyltransferase 3AV5
M.MmuDnmt1 DNA methyltransferase 3AV6
M.MmuDnmt1 DNA methyltransferase 3AV4
M.MmuDnmt1 DNA methyltransferase 3PT6 yes
M.MmuDnmt1 DNA methyltransferase 3PT9
M.MmuDnmt3B DNA methyltransferase 1KHC
M.MpeI DNA methyltransferase 4DKJ yes
M.NtbDRM1 DNA methyltransferase 4ONQ
M.NtbDRM1 DNA methyltransferase 4ONJ
M.PvuII DNA methyltransferase 1BOO
M.RsrI DNA methyltransferase 1NW5
M.RsrI DNA methyltransferase 1NW6
M.RsrI DNA methyltransferase 1NW7
M.RsrI DNA methyltransferase 1NW8
M.RsrI DNA methyltransferase 1EG2
M.SflTDcmP DNA methyltransferase 3ME5
M.SflTDcmP DNA methyltransferase 3LX6
M.Sth18311ORF711P DNA methyltransferase 3LKD
M.TaqI DNA methyltransferase 2JG3 yes
M.TaqI DNA methyltransferase 2NP6 yes
M.TaqI DNA methyltransferase 2NP7 yes
M.TaqI DNA methyltransferase 2IH2 yes
M.TaqI DNA methyltransferase 2IH4 yes
M.TaqI DNA methyltransferase 2IH5 yes
M.TaqI DNA methyltransferase 2IBS yes
M.TaqI DNA methyltransferase 2IBT yes
M.TaqI DNA methyltransferase 1G38 yes
M.TaqI DNA methyltransferase 1AQI
M.TaqI DNA methyltransferase 1AQJ
M.TaqI DNA methyltransferase 2ADM
M.TthHB8ORF409P DNA methyltransferase 2ZIE
M.TthHB8ORF409P DNA methyltransferase 2ZIF
M.TthHB8ORF409P DNA methyltransferase 2ZIG
M.VvuYORF266P DNA methyltransferase 3UFB
M.ZmaIIA DNA methyltransferase 4FSX
M.ZmaIIA DNA methyltransferase 4FT2
M.ZmaIIA DNA methyltransferase 4FT4
M1.DpnII DNA methyltransferase 2DPM
M1.MboII DNA methyltransferase 1G60
Nt.BspD6I Nicking enzyme 2EWF
V.EcoKDcm Nicking enzyme 1ODG yes
V.EcoKDcm Nicking enzyme 1CW0 yes
V.EcoKDcm Nicking enzyme 1VSR
V.MthTI Nicking enzyme 1KEA
AbaSI Restriction endonuclease 4PBB
AbaSI Restriction endonuclease 4PBA yes
AbaSI Restriction endonuclease 4PAR yes
AspBHI Restriction endonuclease 4OC8
BamHI Restriction endonuclease 1ESG yes
BamHI Restriction endonuclease 2BAM yes
BamHI Restriction endonuclease 3BAM yes
BamHI Restriction endonuclease 1BHM yes
BamHI Restriction endonuclease 1BAM
BcnI Restriction endonuclease 2Q10 yes
BcnI Restriction endonuclease 2ODH
BcnI Restriction endonuclease 2ODI yes
BfaSIP Restriction endonuclease 3EVY
BfiI Restriction endonuclease 3ZI5 yes
BfiI Restriction endonuclease 2C1L
BglI Restriction endonuclease 1DMU yes
BglII Restriction endonuclease 1ES8
BglII Restriction endonuclease 1DFM yes
BglII Restriction endonuclease 1D2I yes
BpuJI Restriction endonuclease 2VLA yes
Bse634I Restriction endonuclease 3V1Z yes
Bse634I Restriction endonuclease 3V20 yes
Bse634I Restriction endonuclease 3V21 yes
Bse634I Restriction endonuclease 1KNV
BsoBI Restriction endonuclease 1DC1 yes
BspD6I Restriction endonuclease 2EWF
BspD6I Restriction endonuclease 2P14
BstYI Restriction endonuclease 2P0J yes
BstYI Restriction endonuclease 1VRR yes
BstYI Restriction endonuclease 1SDO
Cfr10I Restriction endonuclease 1CFR
DpnI Restriction endonuclease 4KYW yes
DpnI Restriction endonuclease 4ESJ yes
DraIII Restriction endonuclease 4L0K
Ecl18kI Restriction endonuclease 2GB7 yes
Ecl18kI Restriction endonuclease 2FQZ yes
EcoKMcrBC Restriction endonuclease 3SSD yes
EcoKMcrBC Restriction endonuclease 3SSE yes
EcoKMcrBC Restriction endonuclease 3SSC yes
EcoO109I Restriction endonuclease 1WTD
EcoO109I Restriction endonuclease 1WTE yes
EcoR124I Restriction endonuclease 4BE7
EcoR124I Restriction endonuclease 4BEC
EcoR124I Restriction endonuclease 4BEB
EcoR124I Restriction endonuclease 2W74
EcoR124I Restriction endonuclease 2W00
EcoR124II Restriction endonuclease 2W74
EcoRI Restriction endonuclease 2OXV yes
EcoRI Restriction endonuclease 1QRH yes
EcoRI Restriction endonuclease 1QRI yes
EcoRI Restriction endonuclease 1QPS yes
EcoRI Restriction endonuclease 1QC9
EcoRI Restriction endonuclease 1CL8 yes
EcoRI Restriction endonuclease 1CKQ yes
EcoRI Restriction endonuclease 1ERI yes
EcoRII Restriction endonuclease 3HQF yes
EcoRII Restriction endonuclease 3HQG yes
EcoRII Restriction endonuclease 1NA6
EcoRV Restriction endonuclease 2GE5 yes
EcoRV Restriction endonuclease 2B0D yes
EcoRV Restriction endonuclease 2B0E yes
EcoRV Restriction endonuclease 1SX5 yes
EcoRV Restriction endonuclease 1SX8 yes
EcoRV Restriction endonuclease 1SUZ yes
EcoRV Restriction endonuclease 1STX yes
EcoRV Restriction endonuclease 1EON yes
EcoRV Restriction endonuclease 1EOO yes
EcoRV Restriction endonuclease 1EOP yes
EcoRV Restriction endonuclease 1EO3 yes
EcoRV Restriction endonuclease 1EO4 yes
EcoRV Restriction endonuclease 1B94 yes
EcoRV Restriction endonuclease 1B95 yes
EcoRV Restriction endonuclease 1B96 yes
EcoRV Restriction endonuclease 1B97 yes
EcoRV Restriction endonuclease 1BUA yes
EcoRV Restriction endonuclease 1BSU yes
EcoRV Restriction endonuclease 1BSS yes
EcoRV Restriction endonuclease 1RV5 yes
EcoRV Restriction endonuclease 1BGB yes
EcoRV Restriction endonuclease 1AZ0 yes
EcoRV Restriction endonuclease 1AZ3
EcoRV Restriction endonuclease 1AZ4
EcoRV Restriction endonuclease 1RVA yes
EcoRV Restriction endonuclease 1RVB yes
EcoRV Restriction endonuclease 1RVC yes
EcoRV Restriction endonuclease 4RVE yes
EcoRV Restriction endonuclease 1RVE
EcoRV Restriction endonuclease 2RVE yes
FokI Restriction endonuclease 2FOK
FokI Restriction endonuclease 1FOK yes
HincII Restriction endonuclease 3EBC yes
HincII Restriction endonuclease 3E3Y yes
HincII Restriction endonuclease 3E40 yes
HincII Restriction endonuclease 3E41 yes
HincII Restriction endonuclease 3E42 yes
HincII Restriction endonuclease 3E43 yes
HincII Restriction endonuclease 3E44 yes
HincII Restriction endonuclease 3E45 yes
HincII Restriction endonuclease 2GIE yes
HincII Restriction endonuclease 2GIG yes
HincII Restriction endonuclease 2GIH yes
HincII Restriction endonuclease 2GII yes
HincII Restriction endonuclease 2GIJ yes
HincII Restriction endonuclease 2AUD
HincII Restriction endonuclease 1XHU yes
HincII Restriction endonuclease 1XHV yes
HincII Restriction endonuclease 1TX3 yes
HincII Restriction endonuclease 1TW8 yes
HincII Restriction endonuclease 1KC6 yes
HindIII Restriction endonuclease 3A4K yes
HindIII Restriction endonuclease 2E52 yes
HinP1I Restriction endonuclease 2FL3 yes
HinP1I Restriction endonuclease 2FLC yes
HinP1I Restriction endonuclease 2FKC yes
HinP1I Restriction endonuclease 2FKH yes
HinP1I Restriction endonuclease 1YNM
Hpy188I Restriction endonuclease 3OQG yes
Hpy188I Restriction endonuclease 3OR3 yes
Hpy99I Restriction endonuclease 3FC3 yes
Hpy99I Restriction endonuclease 3GOX yes
MspI Restriction endonuclease 1YFI yes
MspI Restriction endonuclease 1SA3 yes
MspJI Restriction endonuclease 4R28 yes
MspJI Restriction endonuclease 4F0P
MspJI Restriction endonuclease 4F0Q
MunI Restriction endonuclease 1D02 yes
MvaI Restriction endonuclease 2OA9
MvaI Restriction endonuclease 2OAA yes
NaeI Restriction endonuclease 1IAW yes
NaeI Restriction endonuclease 1EV7
NgoAVII Restriction endonuclease 4RDM yes
NgoAVII Restriction endonuclease 4RD5 yes
NgoAVII Restriction endonuclease 4RCT
NgoMIV Restriction endonuclease 4ABT yes
NgoMIV Restriction endonuclease 1FIU yes
NotI Restriction endonuclease 3C25 yes
NotI Restriction endonuclease 3BVQ
OkrAI Restriction endonuclease 3ODH yes
PabI Restriction endonuclease 3WAZ yes
PabI Restriction endonuclease 2DVY
PacI Restriction endonuclease 3M7K yes
PacI Restriction endonuclease 3LDY yes
PspGI Restriction endonuclease 3BM3 yes
PvuII Restriction endonuclease 3KSK
PvuII Restriction endonuclease 1NI0
PvuII Restriction endonuclease 1K0Z
PvuII Restriction endonuclease 1H56
PvuII Restriction endonuclease 1F0O yes
PvuII Restriction endonuclease 1EYU yes
PvuII Restriction endonuclease 2PVI yes
PvuII Restriction endonuclease 3PVI yes
PvuII Restriction endonuclease 1PVU
PvuII Restriction endonuclease 1PVI yes
PvuRts1I Restriction endonuclease 4OKY
PvuRts1I Restriction endonuclease 4OQ2
Sau3AI Restriction endonuclease 2REU
SdaI Restriction endonuclease 2IXS
SfiI Restriction endonuclease 2F03 yes
SfiI Restriction endonuclease 2EZV yes
SgrAI Restriction endonuclease 4C3G yes
SgrAI Restriction endonuclease 3MQ6 yes
SgrAI Restriction endonuclease 3DW9 yes
SgrAI Restriction endonuclease 3DVO yes
SgrAI Restriction endonuclease 3DPG yes
ThaI Restriction endonuclease 3NDH yes
VvuYORF266P Restriction endonuclease 3H1T
S.EcoKI Specificity subunit 2Y7C
S.EcoKI Specificity subunit 2Y7H yes
S.MgeORF438P Specificity subunit 1YDX
S.MjaORF132P Specificity subunit 1YF2
S.TteMORF1547P Specificity subunit 3OKG