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3NKV

Crystal structure of Rab1b covalently modified with AMP at Y77

Functional Information from GO Data
ChainGOidnamespacecontents
A0003924molecular_functionGTPase activity
A0005525molecular_functionGTP binding
B0003924molecular_functionGTPase activity
B0005525molecular_functionGTP binding
Functional Information from PDB Data
site_idAC1
Number of Residues29
DetailsBINDING SITE FOR RESIDUE GNP A 400
ChainResidue
ASER17
AGLU35
ASER36
ASER39
ATHR40
AGLY66
AASN121
ALYS122
AASP124
ALEU125
ASER151
AGLY18
AALA152
ALYS153
AHOH187
AHOH189
AHOH191
AHOH208
AHOH211
AHOH218
AHOH291
AMG500
AVAL19
AGLY20
ALYS21
ASER22
ACYS23
ATYR33
ATHR34

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 500
ChainResidue
ASER22
ATHR40
AHOH189
AHOH218
AGNP400

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE BA A 175
ChainResidue
AILE41
AVAL43
AASP44
AHOH261

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE AMP A 600
ChainResidue
AVAL43
APHE45
AGLN60
ATRP62
ATYR77
AHOH281

site_idAC5
Number of Residues27
DetailsBINDING SITE FOR RESIDUE GNP B 400
ChainResidue
BSER17
BGLY18
BVAL19
BGLY20
BLYS21
BSER22
BCYS23
BTYR33
BGLU35
BTHR40
BGLY66
BASN121
BLYS122
BASP124
BLEU125
BSER151
BALA152
BLYS153
BHOH181
BHOH185
BHOH199
BHOH204
BHOH212
BHOH215
BHOH227
BHOH278
BMG500

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 500
ChainResidue
BSER22
BTHR40
BHOH185
BHOH199
BGNP400

site_idAC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE BA B 175
ChainResidue
AGLU4
AASP6
ATHR56
BASP132
BTHR134
BHOH187
BHOH228
BHOH301

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE AMP B 600
ChainResidue
BPHE45
BTRP62
BTYR77
BHOH176
BHOH216
BHOH256

Functional Information from PROSITE/UniProt
site_idPS00675
Number of Residues14
DetailsSIGMA54_INTERACT_1 Sigma-54 interaction domain ATP-binding region A signature. LLLiGDSGVGKscL
ChainResidueDetails
ALEU11-LEU24

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues20
DetailsBINDING: BINDING => ECO:0000269|PubMed:20651120, ECO:0000269|PubMed:27552051, ECO:0007744|PDB:3NKV, ECO:0007744|PDB:5SZH, ECO:0007744|PDB:5SZK
ChainResidueDetails
ASER17
ALYS153
BSER17
BGLY20
BLYS21
BCYS23
BGLU35
BGLY66
BASN121
BASP124
BALA152
AGLY20
BLYS153
ALYS21
ACYS23
AGLU35
AGLY66
AASN121
AASP124
AALA152

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:27552051, ECO:0007744|PDB:5SZH, ECO:0007744|PDB:5SZK
ChainResidueDetails
AGLY18
ALYS122
BGLY18
BLYS122

site_idSWS_FT_FI3
Number of Residues2
DetailsBINDING: BINDING => ECO:0007744|PDB:3NKV
ChainResidueDetails
AVAL19
BVAL19

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:20651120, ECO:0000269|PubMed:23236136, ECO:0000269|PubMed:27552051, ECO:0007744|PDB:3NKV, ECO:0007744|PDB:4HLQ, ECO:0007744|PDB:4I1O, ECO:0007744|PDB:5SZH, ECO:0007744|PDB:5SZK
ChainResidueDetails
ASER22
ATHR40
BSER22
BTHR40

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:27552051, ECO:0007744|PDB:5SZH
ChainResidueDetails
ATYR33
ASER39
BTYR33
BSER39

site_idSWS_FT_FI6
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:20651120, ECO:0007744|PDB:3NKV
ChainResidueDetails
ATHR34
ASER36
BTHR34
BSER36

site_idSWS_FT_FI7
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:23236136, ECO:0000269|PubMed:27552051, ECO:0007744|PDB:4HLQ, ECO:0007744|PDB:5SZH
ChainResidueDetails
AASP63
BASP63

site_idSWS_FT_FI8
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:27552051, ECO:0007744|PDB:5SZK
ChainResidueDetails
ASER151
BSER151

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: (Microbial infection) O-(2-cholinephosphoryl)serine => ECO:0000269|PubMed:21822290, ECO:0000269|PubMed:22158903, ECO:0000269|PubMed:22307087
ChainResidueDetails
ASER76
BSER76

site_idSWS_FT_FI10
Number of Residues2
DetailsMOD_RES: (Microbial infection) O-AMP-tyrosine => ECO:0000269|PubMed:20651120
ChainResidueDetails
ATYR77
BTYR77

237992

PDB entries from 2025-06-25

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