SMTL ID : 6g56.1

Apo-structure of the alanine racemase from Staphylococcus aureus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: Y.65, N.225, S.226, R.241, G.243, I.244, Y.376 Ligand excluded by PLIP SO4.2: 7 residues within 4Å: Chain A: L.50, H.51, P.52, N.53, K.54, D.233, Q.235 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: Y.250, Q.256, V.261, H.262, L.263, R.358 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: Y.205, K.209, C.234, Q.235, F.236 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: Q.206, K.209 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: S.129, K.130, Q.131, T.168 Ligand excluded by PLIP SO4.7: 7 residues within 4Å: Chain A: S.286, G.288 Chain B: R.160, H.190, F.191, A.192, C.193 Ligand excluded by PLIP SO4.8: 6 residues within 4Å: Chain A: L.37, N.38, A.41, H.75, N.79, D.392 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain B: Y.65, N.225, S.226, G.243, I.244, Y.376 Ligand excluded by PLIP SO4.11: 6 residues within 4Å: Chain B: Y.250, Q.256, V.261, H.262, L.263, R.358 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain B: Y.205, K.209, C.234, Q.235, F.236 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: D.165, T.166, R.207 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: Q.206, K.209, D.210 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: E.171, E.174 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: K.130, K.134, E.171 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain B: G.162, I.163, K.164, D.165, T.168 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: M.232, D.233, C.234 Ligand excluded by PLIP SO4.19: 7 residues within 4Å: Chain B: L.50, H.51, P.52, N.53, K.54, D.233, Q.235 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain B: L.37, N.38, A.41, H.75, N.79 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain B: V.70, K.71, R.74, H.98 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: R.96, H.121, R.122 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain B: K.146, K.147 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: Y.179, E.180, Q.181 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: E.196, S.252, E.253 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: C.333, M.334, D.335, Q.336 Chain B: K.61, R.160 Ligands: GOL.27 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:M.334, A:D.335, A:D.335, A:Q.336, B:K.61, B:R.160, B:R.160 Water bridges: A:Y.306, B:N.225 GOL.26: 6 residues within 4Å: Chain A: K.61 Chain B: Y.287, C.333, M.334, D.335, Q.336 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.306, B:Y.306, B:M.334, B:D.335, B:Q.336, B:Q.336, A:K.61 GOL.27: 7 residues within 4Å: Chain B: K.153, R.160, F.188, H.190, N.225, R.241 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.160, B:H.190, B:N.225, B:R.241

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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