Structure of PDB 2p8b Chain A Binding Site BS02

Receptor Information

>2p8b Chain A (length=369) Species: 226900 (Bacillus cereus ATCC 14579)

MKITAIHLYAIRLPLRNPFVISYGSYSDMPSIIVKMETDEGIIGYGEGVA
DDHVTGESWESTFHTLKHTLTPALIGQNPMNIEKIHDMMDNTIYGVPTAK
AAIDIACFDIMGKKLNQPVYQLIGGRYHEEFPVTHVLSIADPENMAEEAA
SMIQKGYQSFKMKVGTNVKEDVKRIEAVRERVGNDIAIRVDVNQGWKNSA
NTLTALRSLGHLNIDWIEQPVIADDIDAMAHIRSKTDLPLMIDEGLKSSR
EMRQIIKLEAADKVNIKLMKCGGIYPAVKLAHQAEMAGIECQVGSMVESS
VASSAGFHVAFSKKIITSVELTGPLKFTKDIGNLHYDVPFIRLNEKPGLG
IEINEDTLQELTVFQDIVR

Ligand information

• Ligand ID: NSK
• InChI: InChI=1S/C10H18N2O5/c11-6-2-1-3-7(10(16)17)12-8(13)4-5-9(14)15/h7H,1-6,11H2,(H,12,13)(H,14,15)(H,16,17)/t7-/m0/s1
• InChIKey: XEOGRHZGJFTETQ-ZETCQYMHSA-N
• SMILES:
  CACTVS 3.341: NCCCC[C@H](NC(=O)CCC(O)=O)C(O)=O
  ACDLabs 10.04: O=C(NC(C(=O)O)CCCCN)CCC(=O)O
  CACTVS 3.341: NCCCC[CH](NC(=O)CCC(O)=O)C(O)=O
  OpenEye OEToolkits 1.5.0: C(CCN)CC(C(=O)O)NC(=O)CCC(=O)O
  OpenEye OEToolkits 1.5.0: C(CCN)C[C@@H](C(=O)O)NC(=O)CCC(=O)O
• Formula: C10 H18 N2 O5
• Name: N-SUCCINYL LYSINE;
  N~2~-(3-CARBOXYPROPANOYL)-L-LYSINE
• ZINC: ZINC000016052354
• PDB chain: 2p8b Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2p8b Prediction and assignment of function for a divergent N-succinyl amino acid racemase.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): F19 Y26 D51 V136 K161 K163 D243 K267 S295 M296 E320 L321 T322
• Binding residue (residue number reindexed from 1): F19 Y26 D51 V136 K161 K163 D243 K267 S295 M296 E320 L321 T322
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F19 A50 H53 V136 F160 K161 M162 K163 D191 N193 E218 D243 E244 G245 N265 K267 G294 S295 M296 V319 E320 L321
• Catalytic site (residue number reindexed from 1): F19 A50 H53 V136 F160 K161 M162 K163 D191 N193 E218 D243 E244 G245 N265 K267 G294 S295 M296 V319 E320 L321
• Enzyme Commision number: 5.1.1.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016853 isomerase activity
• GO:0016854 racemase and epimerase activity
• GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
• GO:0036361 racemase activity, acting on amino acids and derivatives
• GO:0046872 metal ion binding

Biological Process

• GO:0006518 peptide metabolic process

External links

• PDB: RCSB:2p8b, PDBe:2p8b, PDBj:2p8b
• PDBsum: 2p8b
• PubMed: 17603539
• UniProt: Q81IL5|NSAR_BACCR N-succinyl-L-Arg/Lys racemase (Gene Name=BC_0371)