SMTL ID : 1szu.1

The structure of gamma-aminobutyrate aminotransferase mutant: V241A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-tetramer

Ligands

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: I.184, H.188, R.224 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.224 Salt bridges: A:R.224 SO4.2: 4 residues within 4Å: Chain A: K.151, N.153, Y.394 Chain C: K.192 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.153, A:Y.394 Water bridges: A:K.151 Salt bridges: A:K.151, C:K.192 SO4.9: 2 residues within 4Å: Chain B: K.5, R.381 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.5 Salt bridges: B:K.5, B:R.381 SO4.10: 3 residues within 4Å: Chain B: I.184, H.188, R.224 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.224 Salt bridges: B:H.188, B:R.224 SO4.11: 3 residues within 4Å: Chain B: N.153, Y.394 Chain D: K.192 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain B Salt bridges: D:K.192 Water bridges: B:N.153, B:N.153 SO4.12: 4 residues within 4Å: Chain B: K.192 Chain D: K.151, N.153, Y.394 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.394 Water bridges: D:N.153 Salt bridges: D:K.151, B:K.192 SO4.18: 3 residues within 4Å: Chain C: I.184, H.188, R.224 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.224 SO4.19: 3 residues within 4Å: Chain A: K.192 Chain C: N.153, Y.394 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.394 Water bridges: C:N.153, C:N.153 Salt bridges: A:K.192 SO4.20: 2 residues within 4Å: Chain C: K.71 Chain D: R.29 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Salt bridges: D:R.29, C:K.71 SO4.26: 3 residues within 4Å: Chain D: I.184, H.188, R.224 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.224 SO4.27: 2 residues within 4Å: Chain D: K.5, R.381 6 PLIP interactions: 6 interactions with chain D Water bridges: D:K.5, D:K.5, D:K.5, D:K.5 Salt bridges: D:K.5, D:R.381

14 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: G.164, H.165, V.166, Y.167 Chain C: G.164, H.165, V.166, Y.167 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:H.165, A:Y.167, C:H.165, C:Y.167, C:Y.167 EDO.4: 8 residues within 4Å: Chain A: D.45, A.47, G.48, G.49, H.57 Chain B: T.76, V.80, L.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.49, A:H.57 EDO.5: 5 residues within 4Å: Chain A: Q.69, K.72, L.73, P.85 Chain B: D.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.69, A:K.72 Water bridges: A:K.72 EDO.6: 1 residues within 4Å: Chain A: Q.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.9 EDO.13: 9 residues within 4Å: Chain A: T.76, V.80, L.81 Chain B: D.45, A.47, G.48, G.49, L.53, H.57 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.47, B:G.49, B:H.57 EDO.14: 5 residues within 4Å: Chain B: I.22, H.23, P.24, A.378, R.381 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.23, B:R.381 Water bridges: B:I.22 EDO.15: 9 residues within 4Å: Chain B: G.164, H.165, V.166, Y.167 Chain D: G.164, H.165, V.166, Y.167 Ligands: EDO.31 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:H.165, B:V.166, B:Y.167, D:H.165 Water bridges: D:V.166 EDO.21: 9 residues within 4Å: Chain C: D.45, A.47, G.48, G.49, L.53, H.57 Chain D: T.76, V.80, L.81 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.47, C:G.49, C:H.57 EDO.22: 6 residues within 4Å: Chain C: Q.69, K.72, L.73, P.85 Chain D: A.27, D.28 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.69 Water bridges: C:Q.69, C:K.72, C:K.72, D:D.28 EDO.23: 8 residues within 4Å: Chain C: Q.79, G.292, L.294 Chain D: G.18, V.19, G.20, Q.21, I.22 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:L.294, D:G.20 Water bridges: C:Q.79, D:R.141 EDO.28: 9 residues within 4Å: Chain C: T.76, V.80, L.81 Chain D: D.45, A.47, G.48, G.49, H.57, I.386 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.47, D:G.49, D:H.57 EDO.29: 9 residues within 4Å: Chain C: P.275, N.301, I.303, A.304 Chain D: F.274, P.275, N.301, I.303, A.304 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:N.301, D:A.304, C:N.301, C:A.304 EDO.30: 4 residues within 4Å: Chain D: I.22, H.23, P.24, R.381 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.23, D:R.381 Water bridges: D:I.22 EDO.31: 7 residues within 4Å: Chain B: V.166, Y.167, R.168 Chain D: Y.167, R.168, D.194 Ligands: EDO.15 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Water bridges: B:D.194, D:D.194, D:D.194 Hydrogen bonds: D:R.168

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

PLP.7: 13 residues within 4Å: Chain A: T.110, G.111, S.112, Y.138, H.139, E.206, D.239, A.241, Q.242, K.268 Chain B: G.296, T.297 Ligands: PMP.8 19 PLIP interactions: 5 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:T.297, B:T.297, B:T.297, A:T.110, A:G.111, A:S.112, A:Q.242, A:K.268 Water bridges: B:Y.298, B:A.299, A:S.112, A:S.112, A:Y.138, A:E.206 Hydrophobic interactions: A:E.206, A:A.241, A:K.268 Salt bridges: A:K.268 pi-Stacking: A:Y.138 PLP.16: 14 residues within 4Å: Chain A: E.113, G.296, T.297 Chain B: T.110, G.111, S.112, Y.138, H.139, E.206, D.239, A.241, Q.242, K.268 Ligands: PMP.17 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.206, B:A.241, B:K.268 Hydrogen bonds: B:T.110, B:G.111, B:S.112, B:Q.242, B:K.268, A:T.297, A:T.297 Water bridges: B:T.110, B:T.110, B:Y.138, B:Y.138, B:R.141, B:E.206, A:Y.298, A:Y.298 Salt bridges: B:K.268 pi-Stacking: B:Y.138 PLP.24: 13 residues within 4Å: Chain C: T.110, G.111, S.112, Y.138, H.139, E.206, D.239, A.241, Q.242, K.268 Chain D: G.296, T.297 Ligands: PMP.25 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:E.206, C:K.268 Hydrogen bonds: C:T.110, C:T.110, C:G.111, C:S.112, C:Q.242, D:T.297, D:T.297, D:T.297 Water bridges: C:Y.138, C:A.241, D:Y.298, D:A.299 Salt bridges: C:K.268 pi-Stacking: C:Y.138 PLP.32: 14 residues within 4Å: Chain C: E.113, G.296, T.297 Chain D: T.110, G.111, S.112, Y.138, H.139, E.206, D.239, A.241, Q.242, K.268 Ligands: PMP.33 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain D Hydrogen bonds: C:T.297, C:T.297, C:T.297, D:T.110, D:G.111, D:S.112, D:Q.242 Water bridges: C:Y.298, D:S.112, D:E.206, D:E.211, D:T.265 Hydrophobic interactions: D:E.206, D:A.241, D:K.268 Salt bridges: D:K.268 pi-Stacking: D:Y.138

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

PMP.8: 15 residues within 4Å: Chain A: T.110, G.111, S.112, Y.138, H.139, G.140, E.206, E.211, D.239, A.241, Q.242, K.268 Chain B: G.296, T.297 Ligands: PLP.7 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:T.297, B:T.297, B:T.297, A:T.110, A:G.111, A:S.112, A:Q.242 Water bridges: B:T.297, B:Y.298, B:A.299, A:S.112, A:Y.138, A:R.141 Hydrophobic interactions: A:Y.138, A:E.206 Salt bridges: A:K.268 PMP.17: 13 residues within 4Å: Chain A: T.297 Chain B: T.110, G.111, S.112, Y.138, H.139, E.206, E.211, D.239, A.241, Q.242, K.268 Ligands: PLP.16 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.138, B:E.206 Hydrogen bonds: B:T.110, B:G.111, B:S.112, B:Q.242, A:T.297, A:T.297, A:T.297, A:T.297 Water bridges: B:T.110, B:T.110, B:Y.138, B:Y.138, B:R.141, B:E.206, A:Y.298, A:Y.298 Salt bridges: B:K.268 PMP.25: 15 residues within 4Å: Chain C: T.110, G.111, S.112, Y.138, H.139, G.140, E.206, E.211, D.239, A.241, Q.242, K.268 Chain D: G.296, T.297 Ligands: PLP.24 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:E.206 Hydrogen bonds: C:T.110, C:G.111, C:S.112, C:E.211, C:Q.242, D:T.297, D:T.297, D:T.297, D:T.297 Water bridges: C:Y.138, C:T.265, D:Y.298, D:A.299 Salt bridges: C:K.268 pi-Stacking: C:Y.138 PMP.33: 14 residues within 4Å: Chain C: G.296, T.297 Chain D: T.110, G.111, S.112, Y.138, H.139, E.206, E.211, D.239, A.241, Q.242, K.268 Ligands: PLP.32 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:T.297, C:T.297, C:T.297, C:T.297, D:T.110, D:G.111, D:S.112, D:E.211, D:Q.242 Water bridges: C:Y.298, C:Y.298, D:E.206, D:E.211, D:T.265 Hydrophobic interactions: D:Y.138, D:E.206 Salt bridges: D:K.268

Links

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Citation

Liu, W. et al., Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coligamma-Aminobutyrate Aminotransferase. Biochemistry (2005)

Release Date

2005-03-01

Peptides

4-aminobutyrate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

4-aminobutyrate aminotransferase