SMTL ID : 4ziy.1

Structure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Acinetobacter baumannii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 17 residues within 4Å: Chain A: S.130, S.131, G.132, K.133, T.134, T.135, E.180, N.205, H.300, N.304, R.335, D.349, Y.351, N.352, S.357, K.456 Ligands: MG.2 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.131, A:G.132, A:K.133, A:K.133, A:K.133, A:T.134, A:T.134, A:T.135, A:N.158, A:N.205, A:N.304, A:N.304, A:K.456, A:K.456 Water bridges: A:S.130, A:T.134, A:T.135, A:D.349, A:N.352, A:K.456 Salt bridges: A:R.335 pi-Stacking: A:H.300

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.134, E.180 Ligands: ANP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.134, A:E.180, H2O.9

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: P.21, W.22, Q.26, Y.114, R.115, Q.118 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.26, A:R.115 Water bridges: A:E.20, A:N.119, A:N.119 EDO.4: 3 residues within 4Å: Chain A: D.160, E.188, Y.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.160 Water bridges: A:R.105, A:R.105, A:Y.191 EDO.5: 5 residues within 4Å: Chain A: G.33, Y.34, V.100, V.101, A.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.34 Water bridges: A:T.31, A:E.89, A:A.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Structure of UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase from Acinetobacter baumannii. to be published

Release Date

2015-05-20

Peptides

UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase