SMTL ID : 5fag.1 (1 other biounit)

Alanine Racemase from Streptomyces coelicolor A3(2) with Bound Propionate Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: K.65, Y.69, W.115, K.160, W.198, H.200, N.240, S.241, P.242, R.256, P.257, G.258, I.259, Y.393 Ligands: PPI.6 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.65, A:W.115, A:W.198 Hydrogen bonds: A:Y.69, A:Y.69, A:W.115, A:N.240, A:S.241, A:R.256, A:G.258, A:I.259 Water bridges: A:Y.393, B:Y.302 pi-Stacking: A:H.200 PLP.7: 14 residues within 4Å: Chain B: K.65, Y.69, W.115, K.160, W.198, H.200, N.240, S.241, R.256, P.257, G.258, I.259, Y.393 Ligands: PPI.2 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.65, B:W.115, B:W.198 Hydrogen bonds: B:K.65, B:W.115, B:N.240, B:S.241, B:R.256, B:R.256, B:G.258, B:I.259, B:Y.393 pi-Stacking: B:H.200 Water bridges: A:D.351

5 x PPI: PROPANOIC ACID(Non-covalent)

PPI.2: 9 residues within 4Å: Chain A: Y.302, Y.321, A.349, M.350 Chain B: K.65, Y.69, R.167, Y.393 Ligands: PLP.7 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.302, A:Y.321, A:M.350 Water bridges: A:D.351, A:Q.352, B:R.167 Hydrophobic interactions: B:Y.393 Salt bridges: B:K.65, B:R.167 PPI.6: 9 residues within 4Å: Chain A: K.65, Y.69, R.167, Y.393 Chain B: Y.302, Y.321, A.349, M.350 Ligands: PLP.1 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.393, B:M.350 Water bridges: A:R.167, B:Q.352 Salt bridges: A:K.65, A:R.167 Hydrogen bonds: B:Y.321, B:M.350 PPI.10: 4 residues within 4Å: Chain B: G.173, W.176, E.177, Y.225 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.177 Hydrogen bonds: B:G.173, B:E.177 PPI.11: 3 residues within 4Å: Chain B: P.75, Y.407, E.410 No protein-ligand interaction detected (PLIP) PPI.12: 2 residues within 4Å: Chain B: E.227, R.236 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.236

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

NA.3: 6 residues within 4Å: Chain A: M.61, A.62, V.63, P.257, G.258, M.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.63, A:P.257 NA.4: 8 residues within 4Å: Chain A: A.161, D.162, T.163, G.164, L.165, S.199, H.200, Q.215 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.161, A:T.163, A:G.164, A:L.165, A:Q.215 Water bridges: A:G.166 NA.8: 6 residues within 4Å: Chain B: S.301, A.345, G.346, R.347, F.353, V.354 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.301, B:V.354, B:V.354 NA.9: 8 residues within 4Å: Chain B: A.161, D.162, T.163, G.164, L.165, S.199, H.200, Q.215 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.162, B:T.163, B:G.164, B:L.165, B:S.199, B:Q.215 Water bridges: B:G.166

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 4 residues within 4Å: Chain A: R.45, R.49, A.82, A.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.49, A:A.82 Water bridges: A:A.46 NO3.13: 4 residues within 4Å: Chain B: R.45, R.49, A.82, A.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.49, B:A.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tassoni, R. et al., Structural and functional characterization of the alanine racemase from Streptomyces coelicolor A3(2). Biochem. Biophys. Res. Commun. (2017)

Release Date

2016-12-21

Peptides

Alanine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase

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