SMTL ID : 2vd9.1

The crystal structure of alanine racemase from Bacillus anthracis (BA0252) with bound L-Ala-P

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.334, K.335 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: I.265, D.268 Chain B: K.184 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain B: E.157 No protein-ligand interaction detected (PLIP)

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

CL.3: 3 residues within 4Å: Chain A: N.133, R.140, H.170 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: F.217, Q.218 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: N.133, R.140, H.170 Ligand excluded by PLIP

2 x IN5: {1-[(3-HYDROXY-METHYL-5-PHOSPHONOOXY-METHYL-PYRIDIN-4-YLMETHYL)-AMINO]-ETHYL}-PHOSPHONIC ACID(Non-covalent)

IN5.5: 19 residues within 4Å: Chain A: V.41, K.43, Y.47, L.89, R.140, H.170, N.210, S.211, R.226, I.227, G.228, I.229, Y.361 Chain B: Y.272, Y.291, T.318, M.319, D.320 Ligands: EPC.6 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.89, A:Y.361 Hydrogen bonds: A:K.43, A:Y.47, A:R.140, A:R.140, A:S.211, A:R.226, A:R.226, A:G.228, A:I.229, A:Y.361, A:Y.361, B:Y.272, B:Y.291, B:M.319 Water bridges: A:N.210, A:A.212, B:Y.272, B:D.320, B:D.320 pi-Stacking: A:H.170 IN5.9: 18 residues within 4Å: Chain A: Y.272, Y.291, T.318, M.319, D.320 Chain B: K.43, Y.47, L.89, R.140, H.170, N.210, S.211, R.226, I.227, G.228, I.229, Y.361 Ligands: EPC.10 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.361, A:M.319 Hydrogen bonds: B:K.43, B:Y.47, B:R.140, B:R.140, B:S.211, B:R.226, B:G.228, B:I.229, A:Y.272, A:M.319 Water bridges: B:N.210, B:N.210, A:D.320, A:D.320, A:Q.321 pi-Stacking: B:H.170

2 x EPC: (1S)-1-[((1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLENE)AMINO]ETHYLPHOSPHONIC ACID(Non-covalent)

EPC.6: 17 residues within 4Å: Chain A: K.43, Y.47, L.89, R.140, H.170, N.210, S.211, R.226, G.228, I.229, Y.361 Chain B: Y.272, Y.291, T.318, M.319, D.320 Ligands: IN5.5 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.89, A:Y.361 Hydrogen bonds: A:K.43, A:Y.47, A:Y.47, A:R.140, A:R.140, A:S.211, A:R.226, A:G.228, A:I.229, A:Y.361, B:Y.291, B:M.319, B:D.320 Water bridges: A:N.210, A:A.212, B:Y.272, B:Q.321 pi-Stacking: A:H.170 EPC.10: 18 residues within 4Å: Chain A: Y.272, Y.291, T.318, M.319, D.320 Chain B: V.41, K.43, Y.47, L.89, R.140, H.170, N.210, S.211, R.226, G.228, I.229, Y.361 Ligands: IN5.9 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.89, B:Y.361 Hydrogen bonds: B:K.43, B:R.140, B:R.140, B:S.211, B:R.226, B:G.228, B:I.229, A:Y.272, A:T.318, A:M.319, A:D.320 Water bridges: B:N.210, B:N.210, B:A.212, A:D.320 pi-Stacking: B:H.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Au, K. et al., Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P). Acta Crystallogr.,Sect.F (2008)

Release Date

2008-05-20

Peptides

ALANINE RACEMASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALANINE RACEMASE

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