SMTL ID : 6g59.1

Structure of the alanine racemase from Staphylococcus aureus in complex with an pyridoxal-6- phosphate derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x EM2: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate(Covalent)

EM2.1: 12 residues within 4Å: Chain A: K.61, Y.65, L.107, F.188, H.190, N.225, S.226, R.241, P.242, G.243, I.244, Y.376 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.61, A:L.107, A:L.107, A:F.188 Hydrogen bonds: A:Y.65, A:S.226, A:R.241, A:G.243, A:I.244, A:Y.376 Water bridges: A:K.61, A:N.225, A:A.227 pi-Stacking: A:H.190 EM2.10: 13 residues within 4Å: Chain B: V.59, K.61, Y.65, L.107, F.188, H.190, N.225, S.226, R.241, P.242, G.243, I.244, Y.376 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.61, B:L.107, B:L.107, B:F.188 Hydrogen bonds: B:K.61, B:Y.65, B:S.226, B:R.241, B:G.243, B:I.244 Water bridges: B:R.160, B:A.227, A:D.335 pi-Stacking: B:H.190

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: A.21, G.22, F.23, S.24, K.26 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.22, A:F.23, A:S.24 Water bridges: A:K.26, A:K.26 Salt bridges: A:K.26 SO4.3: 4 residues within 4Å: Chain A: V.70, K.71, R.74, H.98 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:K.71, A:R.74, A:H.98, A:K.404 SO4.4: 4 residues within 4Å: Chain A: H.262, P.265, H.357, R.358 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.358 Water bridges: A:L.263, A:R.358 Salt bridges: A:H.262, A:H.357 SO4.5: 4 residues within 4Å: Chain A: R.312, I.313, Q.315, R.331 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.312 Water bridges: A:R.312 Salt bridges: A:R.331 SO4.11: 6 residues within 4Å: Chain B: H.262, L.263, P.265, H.357, R.358, E.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.358, B:E.359 Salt bridges: B:H.262, B:H.357 SO4.12: 4 residues within 4Å: Chain B: Y.27, Y.32, I.389, R.396 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.396

4 x NA: SODIUM ION(Non-functional Binders)

NA.6: 4 residues within 4Å: Chain A: I.176, Q.177, Y.179, L.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.179 NA.7: 7 residues within 4Å: Chain A: Y.249, P.265, V.267, I.354, D.355, N.356, V.364 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.249, A:V.267, A:D.355 Water bridges: A:V.364 NA.8: 8 residues within 4Å: Chain A: S.284, V.285, S.286, A.289 Chain B: G.157, M.158, A.192, M.200 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.158 NA.13: 3 residues within 4Å: Chain B: I.176, Y.179, L.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.179

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 4 residues within 4Å: Chain A: H.51, P.52, N.53, K.54 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: H.51, P.52, N.53, K.54 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoegl, A. et al., Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics. Nat Chem (2018)

Release Date

2018-05-30

Peptides

Alanine racemase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase 1

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