SMTL ID : 1xql.1

Effect of a Y265F Mutant on the Transamination Based Cycloserine Inactivation of Alanine Racemase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 18 residues within 4Å: Chain A: V.37, K.39, Y.43, L.85, K.129, R.136, H.166, N.203, S.204, R.219, G.221, I.222, Y.354 Chain B: F.265 Ligands: PMH.2, PLP.3, 4AX.6, ACY.10 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.85 Hydrogen bonds: A:Y.43, A:R.136, A:R.136, A:H.166, A:H.166, A:N.203, A:S.204, A:R.219, A:G.221, A:I.222 Water bridges: A:A.205, A:Y.354 pi-Stacking: A:H.166 PMP.7: 17 residues within 4Å: Chain A: F.265 Chain B: V.37, K.39, Y.43, L.85, R.136, H.166, N.203, S.204, R.219, G.221, I.222, Y.354 Ligands: 4AX.4, ACY.5, PMH.8, PLP.9 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.85 Hydrogen bonds: B:Y.43, B:R.136, B:R.136, B:H.166, B:N.203, B:S.204, B:R.219, B:G.221, B:I.222 Water bridges: B:A.205, B:Y.354 pi-Stacking: B:H.166

2 x PMH: (5-HYDROXY-4-{[(3-HYDROXYISOXAZOL-4-YL)AMINO]METHYL}-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

PMH.2: 22 residues within 4Å: Chain A: V.37, K.39, Y.43, L.85, K.129, R.136, H.166, N.203, S.204, R.219, F.220, G.221, I.222, Y.354 Chain B: F.265, Y.284, C.311, M.312 Ligands: PMP.1, PLP.3, 4AX.6, ACY.10 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.85 Hydrogen bonds: A:K.39, A:Y.43, A:R.136, A:R.136, A:H.166, A:H.166, A:N.203, A:S.204, A:R.219, A:R.219, A:G.221, A:I.222, B:Y.284, B:M.312 Water bridges: A:Y.354, B:Q.314, B:Q.314 pi-Cation interactions: A:H.166 PMH.8: 20 residues within 4Å: Chain A: F.265, Y.284, C.311, M.312 Chain B: V.37, K.39, Y.43, L.85, R.136, H.166, N.203, S.204, R.219, G.221, I.222, Y.354 Ligands: 4AX.4, ACY.5, PMP.7, PLP.9 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.85 Hydrogen bonds: B:K.39, B:Y.43, B:R.136, B:R.136, B:H.166, B:N.203, B:S.204, B:R.219, B:R.219, B:G.221, B:I.222, A:Y.284, A:M.312 Water bridges: B:A.205, B:Y.354, A:Y.284, A:I.310 pi-Cation interactions: B:H.166 pi-Stacking: A:F.265

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.3: 18 residues within 4Å: Chain A: V.37, K.39, Y.43, L.85, K.129, R.136, Y.164, H.166, N.203, S.204, R.219, G.221, I.222, Y.354 Ligands: PMP.1, PMH.2, 4AX.6, ACY.10 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.85, A:Y.164 Hydrogen bonds: A:Y.43, A:R.136, A:H.166, A:S.204, A:R.219, A:G.221, A:I.222 Water bridges: A:N.203, A:N.203, A:N.203, A:A.205 pi-Cation interactions: A:H.166 PLP.9: 17 residues within 4Å: Chain B: V.37, K.39, Y.43, L.85, R.136, Y.164, H.166, N.203, S.204, R.219, G.221, I.222, Y.354 Ligands: 4AX.4, ACY.5, PMP.7, PMH.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.85, B:Y.164 Hydrogen bonds: B:Y.43, B:R.136, B:H.166, B:S.204, B:R.219, B:G.221, B:I.222 Water bridges: B:N.203, B:N.203, B:N.203, B:A.205, B:Y.354, B:Y.354 pi-Cation interactions: B:H.166

2 x 4AX: (R)-4-AMINO-ISOXAZOLIDIN-3-ONE(Non-covalent)

4AX.4: 12 residues within 4Å: Chain A: F.265, Y.284, C.311, M.312 Chain B: K.39, Y.43, R.136, Y.354 Ligands: ACY.5, PMP.7, PMH.8, PLP.9 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.284, A:Y.284, A:M.312, B:K.39, B:R.136 Water bridges: A:D.313 4AX.6: 12 residues within 4Å: Chain A: K.39, Y.43, R.136, Y.354 Chain B: F.265, Y.284, C.311, M.312 Ligands: PMP.1, PMH.2, PLP.3, ACY.10 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.39, A:R.136, B:Y.284, B:Y.284, B:M.312 Water bridges: B:Q.314

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.5: 10 residues within 4Å: Chain A: F.265, Y.284, C.311, M.312 Chain B: K.39, R.136 Ligands: 4AX.4, PMP.7, PMH.8, PLP.9 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.284, A:Y.284, A:M.312 Water bridges: A:D.313, A:Q.314 Salt bridges: B:K.39, B:R.136 ACY.10: 10 residues within 4Å: Chain A: K.39, R.136, Y.354 Chain B: F.265, C.311, M.312 Ligands: PMP.1, PMH.2, PLP.3, 4AX.6 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.354 Salt bridges: A:K.39, A:R.136 Hydrogen bonds: B:Y.284, B:Y.284, B:M.312 Water bridges: B:Q.314

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenn, T.D. et al., Effect of a Y265F Mutant on the Transamination-Based Cycloserine Inactivation of Alanine Racemase. Biochemistry (2005)

Release Date

2005-01-18

Peptides

Alanine racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase

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