Structure of PDB 2dve Chain B Binding Site BS01

Receptor Information

>2dve Chain B (length=235) Species: 53953 (Pyrococcus horikoshii)

MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLN
AKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIK
WPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSE
VPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSF
EGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL

Ligand information

• Ligand ID: BT5
• InChI: InChI=1S/C20H28N7O9PS/c21-17-14-18(23-7-22-17)27(8-24-14)19-16(30)15(29)10(35-19)5-34-37(32,33)36-12(28)4-2-1-3-11-13-9(6-38-11)25-20(31)26-13/h7-11,13,15-16,19,29-30H,1-6H2,(H,32,33)(H2,21,22,23)(H2,25,26,31)/t9-,10+,11-,13-,15+,16+,19+/m0/s1
• InChIKey: UTQCSTJVMLODHM-RHCAYAJFSA-N
• SMILES:
  ACDLabs 10.04: O=C1NC2C(SCC2N1)CCCCC(=O)OP(=O)(O)OCC5OC(n3c4ncnc(N)c4nc3)C(O)C5O
  OpenEye OEToolkits 1.7.5: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OC(=O)CCCC[C@H]4[C@@H]5[C@H](CS4)NC(=O)N5)O)O)N
  CACTVS 3.385: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)CCCC[CH]4SC[CH]5NC(=O)N[CH]45)[CH](O)[CH]3O
  CACTVS 3.385: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)OC(=O)CCCC[C@@H]4SC[C@@H]5NC(=O)N[C@H]45)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.7.5: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC(=O)CCCCC4C5C(CS4)NC(=O)N5)O)O)N
• Formula: C20 H28 N7 O9 P S
• Name: BIOTINYL-5-AMP
• ZINC: ZINC000008551918
• PDB chain: 2dve Chain B Residue 1302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2dve Ligand Structures of Biotin Protein Ligase From Pyrococcus Horikoshii OT3
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): S21 T22 Q42 G45 H46 G47 R48 A51 K52 W53 E54 L62 N103 K111 G114 I128 G129 N131 P137
• Binding residue (residue number reindexed from 1): S21 T22 Q42 G45 H46 G47 R48 A51 K52 W53 E54 L62 N103 K111 G114 I128 G129 N131 P137
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): R48 K111 R233
• Catalytic site (residue number reindexed from 1): R48 K111 R233
• Enzyme Commision number: 6.3.4.15: biotin--[biotin carboxyl-carrier protein] ligase.

Gene Ontology

Molecular Function

• GO:0004077 biotin--[biotin carboxyl-carrier protein] ligase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0036211 protein modification process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2dve, PDBe:2dve, PDBj:2dve
• PDBsum: 2dve
• UniProt: O57883