SMTL ID : 2h12.1

Structure of Acetobacter aceti citrate synthase complexed with oxaloacetate and carboxymethyldethia coenzyme A (CMX)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

6 x OAA: OXALOACETATE ION(Non-covalent)

OAA.1: 9 residues within 4Å: Chain A: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Chain B: R.417 Ligands: CMX.9 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.240 Hydrogen bonds: A:R.322, A:R.322 Water bridges: A:A.241, A:H.272, A:H.313, A:H.313 Salt bridges: A:H.237, A:H.237, A:H.272, A:H.313, A:R.322, A:R.396, B:R.417 OAA.10: 9 residues within 4Å: Chain A: R.417 Chain B: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Ligands: CMX.20 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.240 Hydrogen bonds: B:H.237, B:R.322, B:R.322 Water bridges: B:H.272, B:H.313, B:H.313 Salt bridges: B:H.237, B:H.237, B:H.272, B:H.313, B:R.322, B:R.396, A:R.417 OAA.21: 9 residues within 4Å: Chain C: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Chain D: R.417 Ligands: CMX.28 13 PLIP interactions: 1 interactions with chain D, 12 interactions with chain C Salt bridges: D:R.417, C:H.237, C:H.237, C:H.272, C:H.313, C:R.322, C:R.396 Hydrophobic interactions: C:N.240 Hydrogen bonds: C:R.322, C:R.322 Water bridges: C:H.272, C:H.313, C:H.313 OAA.29: 9 residues within 4Å: Chain C: R.417 Chain D: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Ligands: CMX.36 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:N.240 Hydrogen bonds: D:R.322, D:R.322 Water bridges: D:H.272, D:H.313 Salt bridges: D:H.237, D:H.237, D:H.272, D:H.313, D:R.322, D:R.396, C:R.417 OAA.37: 9 residues within 4Å: Chain E: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Chain F: R.417 Ligands: CMX.45 12 PLIP interactions: 1 interactions with chain F, 11 interactions with chain E Salt bridges: F:R.417, E:H.237, E:H.237, E:H.272, E:H.313, E:R.322, E:R.396 Hydrophobic interactions: E:N.240 Hydrogen bonds: E:R.322, E:R.322 Water bridges: E:H.272, E:H.313 OAA.46: 9 residues within 4Å: Chain E: R.417 Chain F: H.237, N.240, H.272, H.313, R.322, F.392, R.396 Ligands: CMX.53 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:N.240 Hydrogen bonds: F:R.322, F:R.322 Water bridges: F:H.313 Salt bridges: F:H.237, F:H.237, F:H.272, F:H.313, F:R.322, F:R.396, E:R.417

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

SO4.2: 4 residues within 4Å: Chain A: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.3: 7 residues within 4Å: Chain A: P.33, I.67, D.68, G.69, D.70, V.315 Chain B: R.419 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: T.114, N.117, H.118 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: D.109, T.110, N.113 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: L.167, R.171 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: P.221, V.222, R.225 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain A: R.133 Chain D: D.135 Ligand excluded by PLIP SO4.11: 7 residues within 4Å: Chain A: R.419 Chain B: P.33, I.67, D.68, G.69, D.70, V.315 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain B: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain A: N.87 Chain B: Y.430, P.432, L.433, R.436 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: T.114, N.117, H.118 Ligand excluded by PLIP SO4.15: 2 residues within 4Å: Chain B: T.110, N.113 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: Y.153, D.155, L.167, R.171 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain B: Q.427 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: P.221, V.222, R.225 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: R.133 Chain E: D.135 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.23: 8 residues within 4Å: Chain C: P.33, I.67, D.68, G.69, D.70, V.315 Chain D: F.48, R.419 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: Y.430, P.432, L.433, R.436 Chain D: E.92 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: T.114, N.117, H.118 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: D.155, L.167, R.171 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: P.221, V.222, R.225 Ligand excluded by PLIP SO4.30: 6 residues within 4Å: Chain C: R.419 Chain D: P.33, I.67, D.68, G.69, D.70 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain D: Y.430, P.432, L.433, R.436 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain D: T.114, N.117, H.118 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain D: L.167, R.171 Ligand excluded by PLIP SO4.35: 2 residues within 4Å: Chain D: P.221, R.225 Ligand excluded by PLIP SO4.38: 4 residues within 4Å: Chain E: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.39: 4 residues within 4Å: Chain E: Y.430, P.432, L.433, R.436 Ligand excluded by PLIP SO4.40: 7 residues within 4Å: Chain E: P.33, I.67, D.68, G.69, D.70, V.315 Chain F: R.419 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain E: T.114, N.117, H.118 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain E: D.109, T.110, N.113 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain E: D.155, R.171 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain E: P.221, R.225 Ligand excluded by PLIP SO4.47: 7 residues within 4Å: Chain E: R.419 Chain F: P.33, I.67, D.68, G.69, D.70, V.315 Ligand excluded by PLIP SO4.48: 4 residues within 4Å: Chain F: H.118, Y.153, R.171, K.175 Ligand excluded by PLIP SO4.49: 3 residues within 4Å: Chain F: T.114, N.117, H.118 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain F: T.110, N.113 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain F: D.155, L.167, R.171 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain F: P.221, R.225 Ligand excluded by PLIP

6 x CMX: CARBOXYMETHYLDETHIA COENZYME *A(Non-covalent)

CMX.9: 23 residues within 4Å: Chain A: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, D.371, F.392 Chain B: R.414, I.415 Ligands: OAA.1 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:A.271, A:K.307, A:L.308, A:L.308, A:G.310, A:F.311, A:F.311, A:Y.360, A:N.369, A:D.371 Water bridges: A:K.317, B:R.414, B:R.414, B:I.415 Salt bridges: A:H.272, A:R.314, A:R.364, B:R.414, B:R.414 pi-Cation interactions: A:K.307, A:K.307 Hydrophobic interactions: B:I.415 CMX.20: 24 residues within 4Å: Chain A: R.414, I.415 Chain B: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, V.370, D.371, F.392 Ligands: OAA.10 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:A.271, B:K.307, B:L.308, B:L.308, B:G.310, B:F.311, B:F.311, B:Y.360, B:N.369, B:D.371 Water bridges: B:R.364, A:R.414, A:R.414, A:R.414, A:R.414, A:I.415 Salt bridges: B:H.272, B:R.314, B:R.364, A:R.414, A:R.414 CMX.28: 24 residues within 4Å: Chain C: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, V.370, D.371, F.392 Chain D: R.414, I.415 Ligands: OAA.21 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:A.271, C:K.307, C:L.308, C:L.308, C:G.310, C:F.311, C:F.311, C:Y.360, C:N.369, C:D.371 Water bridges: C:K.317, D:R.414, D:I.415 Salt bridges: C:H.272, C:R.314, C:R.364, D:R.414, D:R.414 Hydrophobic interactions: D:I.415 CMX.36: 23 residues within 4Å: Chain C: R.414, I.415 Chain D: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, D.371, F.392 Ligands: OAA.29 23 PLIP interactions: 7 interactions with chain C, 16 interactions with chain D Hydrophobic interactions: C:I.415 Water bridges: C:R.414, C:R.414, C:R.414, C:I.415, D:R.364, D:R.364 Salt bridges: C:R.414, C:R.414, D:H.272, D:R.314, D:R.364 Hydrogen bonds: D:A.271, D:K.307, D:L.308, D:L.308, D:G.310, D:F.311, D:F.311, D:Y.360, D:N.369, D:D.371 pi-Cation interactions: D:K.307 CMX.45: 24 residues within 4Å: Chain E: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, V.370, D.371, F.392 Chain F: R.414, I.415 Ligands: OAA.37 23 PLIP interactions: 17 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:A.271, E:K.307, E:K.307, E:L.308, E:L.308, E:G.310, E:F.311, E:F.311, E:Y.360, E:N.369, E:D.371 Water bridges: E:R.364, F:R.414, F:R.414, F:R.414, F:I.415 Salt bridges: E:H.272, E:R.314, E:R.364, F:R.414, F:R.414 pi-Cation interactions: E:K.307, E:K.307 CMX.53: 23 residues within 4Å: Chain E: R.414, I.415 Chain F: P.270, A.271, H.272, G.273, A.275, V.299, K.307, L.308, M.309, G.310, F.311, G.312, H.313, R.314, Y.360, R.364, L.366, N.369, D.371, F.392 Ligands: OAA.46 23 PLIP interactions: 17 interactions with chain F, 6 interactions with chain E Hydrogen bonds: F:A.271, F:K.307, F:L.308, F:L.308, F:G.310, F:F.311, F:F.311, F:Y.360, F:N.369, F:D.371 Water bridges: F:K.307, F:K.307, F:K.307, F:K.317, E:R.414, E:R.414, E:I.415, E:I.415 Salt bridges: F:H.272, F:R.314, F:R.364, E:R.414, E:R.414

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Francois, J.A. et al., Structure of a NADH-insensitive hexameric citrate synthase that resists acid inactivation. Biochemistry (2006)

Release Date

2006-09-26

Peptides

Citrate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Citrate synthase