SMTL ID : 5irp.1

Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: N.132, R.139, L.140 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: S.371, R.372 Chain B: S.371, R.372 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.107, W.110 Chain B: Q.335 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: Y.272, R.297, R.317 Ligands: TRS.22 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: N.132, R.139, L.140 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: Q.335 Chain B: Q.107, W.110 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain B: Y.272, R.297, R.317 Ligands: TRS.3 Ligand excluded by PLIP

2 x UAH: (5-hydroxy-6-methylpyridin-3-yl)methyl dihydrogen phosphate(Non-covalent)

UAH.2: 13 residues within 4Å: Chain A: V.37, K.39, Y.43, L.85, R.139, H.169, N.209, T.210, R.225, G.227, I.228, Y.364 Ligands: CO2.23 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.85 Hydrogen bonds: A:Y.43, A:R.139, A:R.139, A:T.210, A:R.225, A:R.225, A:G.227, A:I.228 Water bridges: A:K.39, A:Y.43, A:N.209, A:N.209, A:A.211 pi-Cation interactions: A:H.169 UAH.21: 13 residues within 4Å: Chain B: V.37, K.39, Y.43, L.85, R.139, H.169, N.209, T.210, R.225, G.227, I.228, Y.364 Ligands: CO2.19 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.85 Hydrogen bonds: B:K.39, B:Y.43, B:R.139, B:T.210, B:R.225, B:R.225, B:G.227, B:I.228 Water bridges: B:K.39, B:R.139, B:N.209, B:N.209, B:A.211 pi-Cation interactions: B:H.169

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 6 residues within 4Å: Chain A: D.174, N.209, P.235, Y.364 Chain B: Y.272 Ligands: CL.37 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.364 Water bridges: A:N.209, A:N.209, A:N.209, A:P.235, A:Y.364, B:Y.272, B:R.317, B:R.317 TRS.22: 5 residues within 4Å: Chain A: Y.272 Chain B: D.174, P.235, Y.364 Ligands: CL.16 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.364 Water bridges: B:N.209, B:N.209, B:N.209, B:Y.364, A:Y.272

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: R.126, K.159, F.160 No protein-ligand interaction detected (PLIP) PEG.5: 3 residues within 4Å: Chain A: L.192, S.193, K.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.196 Water bridges: A:S.193, A:K.196 PEG.24: 5 residues within 4Å: Chain B: S.123, A.124, R.126, K.159, F.160 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.126 PEG.25: 3 residues within 4Å: Chain B: I.189, L.192, K.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.196

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: E.329, N.330, G.331, E.332 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.332 Water bridges: A:K.310, A:E.329 GOL.26: 4 residues within 4Å: Chain B: K.310, L.327, E.329, N.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.310, B:L.327 Water bridges: B:E.332

20 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.9: 1 residues within 4Å: Chain A: N.301 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.301, H2O.10 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: Q.107 Chain B: Y.259 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain A: R.126, L.155, K.156, S.158, L.161 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.155, A:S.158, A:L.161, H2O.6, H2O.10 MG.13: 1 residues within 4Å: Chain A: Q.241 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain A: Y.276, I.277, E.279, E.282 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain A: M.1, E.11, E.338 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain A: P.249 No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain B: Q.107 No protein-ligand interaction detected (PLIP) MG.33: 4 residues within 4Å: Chain B: L.155, K.156, S.158, L.161 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.155, B:S.158, B:L.161, H2O.23 MG.34: 4 residues within 4Å: Chain B: A.97, N.100, N.125, R.126 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.97, B:R.126, H2O.16 MG.35: 3 residues within 4Å: Chain B: Y.276, E.279, E.282 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.282, H2O.22 MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.38: 3 residues within 4Å: Chain B: M.1, E.11, E.338 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain B: P.249 No protein-ligand interaction detected (PLIP)

2 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.19: 7 residues within 4Å: Chain A: Y.272, T.319, M.320 Chain B: K.39, R.139, H.169 Ligands: UAH.21 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.320, B:K.39, B:R.139, B:R.139 Water bridges: A:Y.291, A:D.321 CO2.23: 7 residues within 4Å: Chain A: K.39, R.139, H.169 Chain B: Y.272, T.319, M.320 Ligands: UAH.2 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.320, A:K.39, A:R.139, A:R.139 Water bridges: B:Y.291, B:D.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bernardo-Garcia, N. et al., Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org.Biomol.Chem. (2019)

Release Date

2017-03-29

Peptides

Alanine racemase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase 2

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