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

Alanine Racemase from Streptomyces coelicolor A3(2) in complex with D-Cycloserine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x DCS: D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE(Non-covalent)

DCS.1: 18 residues within 4Å: Chain A: K.65, Y.69, W.115, R.167, W.198, H.200, N.240, S.241, P.242, R.256, P.257, G.258, I.259, Y.393 Chain B: Y.302, Y.321, A.349, M.350 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.115, A:W.198 Hydrogen bonds: A:K.65, A:Y.69, A:Y.69, A:R.167, A:N.240, A:S.241, A:R.256, A:G.258, A:I.259, B:M.350 Water bridges: A:K.65, B:Y.302, B:Y.302, B:Q.352, B:Q.352 pi-Stacking: A:H.200 DCS.4: 18 residues within 4Å: Chain A: Y.302, Y.321, A.349, M.350 Chain B: K.65, Y.69, W.115, R.167, W.198, H.200, N.240, S.241, P.242, R.256, P.257, G.258, I.259, Y.393 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.115, B:W.198 Hydrogen bonds: B:K.65, B:Y.69, B:R.167, B:R.167, B:N.240, B:S.241, B:R.256, B:R.256, B:G.258, B:I.259, B:Y.393, A:Y.302, A:Y.321, A:M.350, A:D.351 Water bridges: B:K.65, B:W.115, A:Q.352 pi-Stacking: B:H.200

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

NA.2: 9 residues within 4Å: Chain A: A.161, D.162, T.163, G.164, L.165, S.199, H.200, Q.215 Ligands: CL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.161, A:T.163, A:G.164, A:L.165, A:H.200, A:Q.215 NA.5: 9 residues within 4Å: Chain B: A.161, D.162, T.163, G.164, L.165, S.199, H.200, Q.215 Ligands: CL.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:A.161, B:D.162, B:T.163, B:G.164, B:L.165, B:H.200, B:Q.215

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

CL.3: 8 residues within 4Å: Chain A: K.160, D.162, L.165, G.166, R.167, G.168, G.169 Ligands: NA.2 Ligand excluded by PLIP CL.6: 8 residues within 4Å: Chain B: K.160, D.162, L.165, G.166, R.167, G.168, G.169 Ligands: NA.5 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: H.305, S.330, S.331, G.346, R.347 Ligand excluded by PLIP

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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