SMTL ID : 6g58.1

Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x EOW: (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate(Covalent)

EOW.1: 15 residues within 4Å: Chain A: V.59, K.61, Y.65, L.107, K.153, R.160, H.190, N.225, S.226, R.241, P.242, G.243, I.244, Y.376 Ligands: ACT.24 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.61, A:L.107, A:L.107, A:H.190 Hydrogen bonds: A:K.61, A:Y.65, A:S.226, A:R.241, A:G.243, A:I.244, A:Y.376, A:Y.376, A:Y.376 Water bridges: A:R.160, A:N.225, A:N.225, A:A.227 pi-Cation interactions: A:H.190 EOW.13: 15 residues within 4Å: Chain B: K.61, Y.65, L.107, K.153, R.160, F.188, H.190, N.225, S.226, R.241, P.242, G.243, I.244, Y.376 Ligands: ACT.8 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.61, B:L.107, B:L.107, B:F.188, B:H.190 Hydrogen bonds: B:K.61, B:S.226, B:S.226, B:R.241, B:G.243, B:I.244, B:Y.376 Water bridges: B:R.160, B:N.225, B:N.225, B:A.227, A:D.335 pi-Cation interactions: B:H.190

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

NA.2: 3 residues within 4Å: Chain A: N.381, S.383 Chain B: N.381 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.380 NA.3: 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:L.182 NA.4: 4 residues within 4Å: Chain A: Y.287, Y.306 Chain B: I.374 Ligands: ACT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.306 NA.14: 4 residues within 4Å: Chain B: I.176, Q.177, Y.179, L.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.176 NA.15: 4 residues within 4Å: Chain A: I.374 Chain B: Y.287, Y.306 Ligands: ACT.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.306, B:Y.306 NA.16: 2 residues within 4Å: Chain B: Q.235, C.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.235

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 4 residues within 4Å: Chain A: R.312, I.313, Q.315, R.331 No protein-ligand interaction detected (PLIP) MPD.6: 4 residues within 4Å: Chain A: L.230, L.231, M.232, D.233 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.231 Water bridges: A:K.258 MPD.7: 4 residues within 4Å: Chain A: R.96, T.101, R.122, W.149 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.122, A:W.149 MPD.18: 4 residues within 4Å: Chain B: R.312, I.313, Q.315, R.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.370, B:K.370 MPD.19: 7 residues within 4Å: Chain A: Y.27, Y.28, R.29, S.30 Chain B: P.111, K.113, D.114 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.111, B:K.113, A:Y.27 Hydrogen bonds: B:K.113, B:D.114 MPD.20: 5 residues within 4Å: Chain B: R.96, T.101, A.102, R.122, W.149 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.122, B:W.149 MPD.21: 4 residues within 4Å: Chain B: P.52, N.53, K.54, T.55 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.53 Water bridges: B:T.55 MPD.22: 4 residues within 4Å: Chain B: R.74, E.78, G.99, T.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.78 Water bridges: B:R.74

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 8 residues within 4Å: Chain A: Y.287, Y.306, C.333, M.334 Chain B: K.61, Y.376 Ligands: NA.4, EOW.13 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.376, A:Y.287 Water bridges: B:R.160, A:D.335, A:Q.336 Salt bridges: B:K.61 Hydrogen bonds: A:Y.287, A:M.334 ACT.9: 4 residues within 4Å: Chain A: N.272, V.273, G.348 Chain B: P.111 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.111 ACT.10: 5 residues within 4Å: Chain A: N.53, K.54, Q.235, C.237, N.238 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.53, A:N.238 Salt bridges: A:K.54 ACT.11: 1 residues within 4Å: Chain A: K.258 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.258 ACT.12: 4 residues within 4Å: Chain A: Y.27, Y.32, I.389, R.396 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.32 Hydrogen bonds: A:Y.27, A:Y.27 Salt bridges: A:R.396 ACT.24: 8 residues within 4Å: Chain A: K.61, Y.376 Chain B: Y.287, Y.306, C.333, M.334 Ligands: EOW.1, NA.15 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.376 Water bridges: A:R.160, A:R.160, B:Q.336 Salt bridges: A:K.61 Hydrogen bonds: B:Y.306, B:Y.306, B:M.334

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

CL.17: 3 residues within 4Å: Chain B: K.153, M.158, R.160 Ligand excluded by PLIP

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.23: 4 residues within 4Å: Chain B: I.140, Y.179, Q.181, L.182 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.140, B:I.140, B:Y.179, B:L.182 Water bridges: B:Q.181, B:Q.181

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.25: 6 residues within 4Å: Chain A: V.274, P.303, Q.336 Chain B: G.108, V.109, L.161 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:R.29, A:P.303, A:Q.336, A:Q.336, A:Q.336, A:Q.336 Hydrogen bonds: B:V.109, B:V.109

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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