Structure of PDB 3glm Chain B Binding Site BS01

Receptor Information

>3glm Chain B (length=562) Species: 1512 ([Clostridium] symbiosum)

MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITS
EEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGR
VDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSG
VEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSI
SPTILIAHQDANMAVGGAGAEQIIAAQIENSKLKVPAPGSVPIHYDETGF
FREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIP
MNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIAN
VQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDT
TGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGG
PQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAQPIIGKMNDMIQ
MYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQM
LTPRSTREFETF

Ligand information

• Ligand ID: COO
• InChI: InChI=1S/C25H40N7O17P3S/c1-4-5-16(34)53-9-8-27-15(33)6-7-28-23(37)20(36)25(2,3)11-46-52(43,44)49-51(41,42)45-10-14-19(48-50(38,39)40)18(35)24(47-14)32-13-31-17-21(26)29-12-30-22(17)32/h4-5,12-14,18-20,24,35-36H,6-11H2,1-3H3,(H,27,33)(H,28,37)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,18-,19-,20?,24-/m1/s1
• InChIKey: KFWWCMJSYSSPSK-XBTRWLRFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC=CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.341: CC=CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  CACTVS 3.341: CC=CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(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
  ACDLabs 10.04: O=C(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)/C=C/C
  OpenEye OEToolkits 1.5.0: CC=CC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(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)O
• Formula: C25 H40 N7 O17 P3 S
• Name: CROTONYL COENZYME A
• PDB chain: 3glm Chain B Residue 590

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3glm An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): R59 M118 A119 S151 G152 V153 E154 F155 Y162 T192 A195 G196
• Binding residue (residue number reindexed from 1): R57 M116 A117 S149 G150 V151 E152 F153 Y160 T190 A193 G194
• Annotation score: 3

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 I403 A443 A444
• 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

External links

• PDB: RCSB:3glm, PDBe:3glm, PDBj:3glm
• PDBsum: 3glm
• PubMed: 19654317
• UniProt: B7TVP1