SMTL ID : 6h5e.2 (1 other biounit)

Crystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus with bound AMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.1: 2 residues within 4Å: Chain A: D.138, T.159 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.138, A:T.159 Water bridges: A:D.138, A:T.139 Salt bridges: A:D.138

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: N.127, R.128, R.152, Y.167, D.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.127, A:R.152 GOL.3: 4 residues within 4Å: Chain A: F.165, G.166, Y.167, K.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.166, A:K.174, A:K.174 GOL.4: 6 residues within 4Å: Chain A: C.208, E.209, I.213, P.214, F.215, K.218 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.208, A:E.209, A:F.215, A:E.216, A:K.218 GOL.9: 4 residues within 4Å: Chain A: N.148 Chain B: G.347, R.348, D.349 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.348, B:D.349, B:D.349 Water bridges: A:N.148 GOL.10: 3 residues within 4Å: Chain B: E.151, S.154, N.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.151, B:S.154, B:N.155

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: D.221, E.223, A.224, Q.227 Chain B: Q.380, K.384 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.221, A:E.223, A:A.224, A:Q.227, B:Q.380 PEG.11: 4 residues within 4Å: Chain B: D.212, H.221, Y.222, R.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.222, B:R.230 PEG.12: 5 residues within 4Å: Chain B: R.396, D.397, I.398, Y.399, P.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.396, B:I.398

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.202, C.205, C.224, C.226 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.202, B:C.205, B:C.224, B:C.226

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

ANP.7: 15 residues within 4Å: Chain B: T.56, N.57, G.58, K.59, T.60, T.61, N.85, E.108, N.130, F.132, Y.216, F.263, Y.266, N.267 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.56, B:N.57, B:G.58, B:K.59, B:K.59, B:K.59, B:T.60, B:T.61, B:T.61, B:N.85, B:N.130, B:Y.216, B:N.267, B:N.267 Water bridges: B:K.59

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain B: T.60, E.108 Ligands: ANP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.60, B:E.108, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noldeke, E.R. et al., Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus. Sci Rep (2018)

Release Date

2018-09-05

Peptides

SA1707 protein: A
DUF1727 domain-containing protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

SA1707 protein

DUF1727 domain-containing protein

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