Structure of PDB 3gma Chain B Binding Site BS01

Receptor Information
>3gma Chain B (length=566) Species: 1512 ([Clostridium] symbiosum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITS
EEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGR
VDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSG
VEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSI
SPTILIAHQDANMAVGGAGDDEAAEQIIAAQIENSKLKVPAPGSVPIHYD
ETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLY
SIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVG
VIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIW
LQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHY
VLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAQPIIGKMN
DMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICP
MHQMLTPRSTREFETF
Ligand information
Ligand IDGRA
InChIInChI=1S/C26H42N7O19P3S/c1-26(2,21(39)24(40)29-7-6-15(34)28-8-9-56-17(37)5-3-4-16(35)36)11-49-55(46,47)52-54(44,45)48-10-14-20(51-53(41,42)43)19(38)25(50-14)33-13-32-18-22(27)30-12-31-23(18)33/h12-14,19-21,25,38-39H,3-11H2,1-2H3,(H,28,34)(H,29,40)(H,35,36)(H,44,45)(H,46,47)(H2,27,30,31)(H2,41,42,43)/t14-,19-,20-,21+,25-/m1/s1
InChIKeySYKWLIJQEHRDNH-CKRMAKSASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CCCC(=O)O)O
ACDLabs 10.04O=C(O)CCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)CCCC(=O)O)O
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CCCC(O)=O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CCCC(O)=O
FormulaC26 H42 N7 O19 P3 S
Nameglutaryl-coenzyme A
ChEMBL
DrugBank
ZINCZINC000008551192
PDB chain3gma Chain B Residue 589 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3gma An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases
Resolution2.6 Å
Binding residue
(original residue number in PDB)		M118 S151 G152 V153 E154 F155 T192 A195 G196
Binding residue
(residue number reindexed from 1)		M116 S149 G150 V151 E152 F153 T190 A193 G194
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) V153 A195 G196 I420 A460 A461
Catalytic site (residue number reindexed from 1) V151 A193 G194 I407 A447 A448
Enzyme Commision number 4.1.1.70: Transferred entry: 7.2.4.5.
Gene Ontology
Molecular Function
GO:0004485 methylcrotonoyl-CoA carboxylase activity
GO:0016874 ligase activity
Biological Process
GO:0006552 L-leucine catabolic process
Cellular Component
GO:1905202 methylcrotonoyl-CoA carboxylase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3gma, PDBe:3gma, PDBj:3gma
PDBsum3gma
PubMed19654317
UniProtB7TVP1

[Back to BioLiP]