SMTL ID : 1sff.1

Structure of gamma-aminobutyrate aminotransferase complex with aminooxyacetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.151, N.153, Y.394 Chain C: K.192 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A Salt bridges: C:K.192, A:K.151 Hydrogen bonds: A:N.153 Water bridges: A:K.151, A:K.151, A:K.151, A:K.151, A:N.153, A:N.153, A:P.392 SO4.2: 2 residues within 4Å: Chain A: I.184, R.224 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.181, A:R.224 Salt bridges: A:R.224 SO4.8: 3 residues within 4Å: Chain B: K.151, N.153, Y.394 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.151, B:K.151, B:N.153 Salt bridges: B:K.151 SO4.9: 3 residues within 4Å: Chain B: K.5, P.24, R.381 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.5, B:K.5 Salt bridges: B:K.5, B:R.381 SO4.10: 2 residues within 4Å: Chain B: I.184, R.224 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.224 Salt bridges: B:R.224 SO4.15: 4 residues within 4Å: Chain A: K.192 Chain C: K.151, N.153, Y.394 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.153, C:Y.394 Water bridges: C:K.151, C:K.151, C:N.153, C:N.153, A:K.192 Salt bridges: C:K.151, A:K.192 SO4.16: 2 residues within 4Å: Chain C: I.184, R.224 3 PLIP interactions: 3 interactions with chain C Water bridges: C:H.188, C:R.224 Salt bridges: C:R.224 SO4.17: 2 residues within 4Å: Chain C: K.71 Chain D: R.29 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Water bridges: D:R.29, D:R.29, D:R.29 Salt bridges: D:R.29, C:K.71 SO4.22: 4 residues within 4Å: Chain B: K.192 Chain D: K.151, N.153, Y.394 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain D Salt bridges: B:K.192, D:K.151 Hydrogen bonds: D:N.153, D:Y.394 Water bridges: D:K.151, D:K.151, D:N.153, D:P.392 SO4.23: 3 residues within 4Å: Chain D: K.5, P.24, 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 SO4.24: 2 residues within 4Å: Chain D: H.188, R.224 2 PLIP interactions: 2 interactions with chain D Water bridges: D:H.188 Salt bridges: D:R.224

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

EDO.3: 9 residues within 4Å: Chain A: D.45, A.47, G.48, G.49, L.53, 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.4: 6 residues within 4Å: Chain A: Q.69, K.72, L.73, P.85 Chain B: A.27, D.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.69, A:K.72, A:K.72 EDO.5: 9 residues within 4Å: Chain A: G.164, H.165, V.166, Y.167 Chain C: G.164, H.165, V.166, Y.167 Ligands: EDO.20 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:H.165, C:Y.167, C:Y.167, A:H.165, A:H.165, A:Y.167 Water bridges: C:V.166, C:V.166, A:V.166 EDO.6: 1 residues within 4Å: Chain A: Q.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.9 EDO.11: 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.49, B:H.57 EDO.12: 8 residues within 4Å: Chain B: G.164, H.165, V.166, Y.167 Chain D: G.164, H.165, V.166, Y.167 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:H.165, B:H.165, B:Y.167, D:H.165, D:Y.167 Water bridges: B:V.166, B:V.166, D:V.166 EDO.13: 4 residues within 4Å: Chain B: I.22, H.23, P.24, R.381 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.23, B:R.381 EDO.18: 8 residues within 4Å: Chain C: D.45, A.47, G.48, G.49, H.57 Chain D: T.76, V.80, L.81 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.49, C:H.57 EDO.19: 6 residues within 4Å: Chain C: Q.69, K.72, L.73, P.85 Chain D: A.27, D.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.69, C:K.72 EDO.20: 6 residues within 4Å: Chain A: A.147, M.162, P.163 Chain C: Y.167, D.194 Ligands: EDO.5 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Y.167, C:Y.167, A:A.147, A:M.162 Water bridges: A:R.168 EDO.25: 8 residues within 4Å: Chain C: T.76, V.80, L.81 Chain D: D.45, A.47, G.48, G.49, H.57 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.49, D:H.57 EDO.26: 7 residues within 4Å: Chain C: A.27, D.28 Chain D: Q.69, K.72, L.73, Y.83, P.85 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.69, D:K.72 Water bridges: D:Q.69 EDO.27: 4 residues within 4Å: Chain D: I.22, H.23, P.24, R.381 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.23, D:R.381 EDO.28: 7 residues within 4Å: Chain C: P.275, N.301, I.303 Chain D: F.274, P.275, N.301, I.303 No protein-ligand interaction detected (PLIP)

4 x IK2: 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

IK2.7: 16 residues within 4Å: Chain A: T.110, G.111, S.112, Y.138, H.139, G.140, R.141, E.206, E.211, D.239, V.241, Q.242, K.268 Chain B: Q.79, G.296, T.297 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.138, A:E.206, A:V.241 Hydrogen bonds: A:T.110, A:G.111, A:S.112, A:Y.138, A:Q.242, A:K.268, A:K.268, B:G.296, B:T.297 Water bridges: A:S.112, A:Y.138, A:R.141, A:E.206, A:E.211, B:Y.298 Salt bridges: A:R.141 IK2.14: 16 residues within 4Å: Chain A: Q.79, G.296, T.297 Chain B: T.110, G.111, S.112, Y.138, H.139, G.140, R.141, E.206, E.211, D.239, V.241, Q.242, K.268 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.138, B:E.206, B:V.241 Hydrogen bonds: B:G.111, B:S.112, B:Y.138, B:K.268, B:K.268, A:Q.79, A:G.296, A:T.297 Water bridges: B:T.110, B:T.110, B:S.112, B:Y.138, B:R.141, B:E.206, A:Y.298 Salt bridges: B:R.141 IK2.21: 16 residues within 4Å: Chain C: T.110, G.111, S.112, Y.138, H.139, G.140, R.141, E.206, E.211, D.239, V.241, Q.242, K.268 Chain D: Q.79, G.296, T.297 19 PLIP interactions: 5 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:Q.79, D:G.296, D:T.297, D:T.297, C:T.110, C:G.111, C:S.112, C:E.211, C:K.268, C:K.268 Water bridges: D:Y.298, C:S.112, C:Y.138, C:E.206, C:E.211 Hydrophobic interactions: C:Y.138, C:E.206, C:V.241 Salt bridges: C:R.141 IK2.29: 16 residues within 4Å: Chain C: Q.79, G.296, T.297 Chain D: T.110, G.111, S.112, Y.138, H.139, G.140, R.141, E.206, E.211, D.239, V.241, Q.242, K.268 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.138, D:E.206, D:V.241 Hydrogen bonds: D:G.111, D:S.112, D:E.211, D:K.268, D:K.268, C:Q.79, C:G.296, C:T.297, C:T.297 Water bridges: D:T.110, D:T.110, D:S.112, D:Y.138, D:E.211, D:Q.242, C:Y.298 Salt bridges: D:R.141

Links

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Citation

Liu, W. et al., Crystal structures of unbound and aminooxyacetate-bound Escherichia coli gamma-aminobutyrate aminotransferase. Biochemistry (2004)

Release Date

2004-09-14

Peptides

4-aminobutyrate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

4-aminobutyrate aminotransferase

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