Structure of PDB 2yzn Chain C Binding Site BS01

Receptor Information
>2yzn Chain C (length=309) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAPGRAELLIPAPLDPGTQETVQELALKAYKV
LGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELL
RRLVELALT
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain2yzn Chain C Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2yzn Crystal structure of D-alanine:D-Alanine Ligase with AMPPNP from Thermus thermophilus HB8
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K116 F151 K153 S159 A191 L192 E197 F272 E282
Binding residue
(residue number reindexed from 1)		K116 F151 K153 S159 A191 L192 E197 F262 E272
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E13 V16 L19 H82 S159 R268 D270 E282 N284 G288 T292
Catalytic site (residue number reindexed from 1) E13 V16 L19 H82 S159 R258 D260 E272 N274 G278 T282
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2yzn, PDBe:2yzn, PDBj:2yzn
PDBsum2yzn
PubMed
UniProtQ5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)

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