Structure of PDB 4q3b Chain D Binding Site BS01

Receptor Information
>4q3b Chain D (length=260) Species: 269797 (Methanosarcina barkeri str. Fusaro) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVG
IVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEI
ILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGL
GKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSI
IFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGI
GTASMLYSVL
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain4q3b Chain D Residue 901 [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]
PDB4q3b The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed by Pyrrolysine Synthase (PylD).
Resolution1.9 Å
Binding residue
(original residue number in PDB)		N121 T125 K151 V152 Y170 D171 A172 A203 T204 P205 C206 P224 I226 P246 L247
Binding residue
(residue number reindexed from 1)		N122 T126 K152 V153 Y171 D172 A173 A204 T205 P206 C207 P225 I227 P247 L248
Annotation score4
Enzymatic activity
Enzyme Commision number 1.4.1.-
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
Biological Process
GO:0008652 amino acid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4q3b, PDBe:4q3b, PDBj:4q3b
PDBsum4q3b
PubMed24916332
UniProtQ46E80|PYLD_METBF Pyrrolysine synthase (Gene Name=pylD)

[Back to BioLiP]