SMTL ID : 1nxg.1

The F383A variant of type II Citrate Synthase complexed with NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: N.233, A.234, R.300, R.307 Chain B: I.406, R.408 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.234 Water bridges: A:S.235, A:R.307, A:R.307 Salt bridges: A:R.300, A:R.307, B:R.408 SO4.2: 7 residues within 4Å: Chain A: H.230, N.233, L.260, R.300, H.306, R.315, R.388 10 PLIP interactions: 10 interactions with chain A Water bridges: A:H.230, A:H.306, A:H.306, A:R.315, A:D.363 Salt bridges: A:H.230, A:R.300, A:H.306, A:R.315, A:R.388 SO4.4: 6 residues within 4Å: Chain A: I.406, R.408 Chain B: N.233, A.234, R.300, R.307 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.234 Water bridges: B:R.300 Salt bridges: B:R.300, B:R.307, A:R.408 SO4.5: 6 residues within 4Å: Chain B: H.230, N.233, H.306, R.315, D.363, R.388 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.300 Water bridges: B:H.230 Salt bridges: B:H.230, B:H.306, B:R.315, B:R.388 SO4.7: 6 residues within 4Å: Chain C: N.233, A.234, R.300, R.307 Chain D: I.406, R.408 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.234 Water bridges: C:S.235, C:R.307, C:R.307 Salt bridges: C:R.300, C:R.307, D:R.408 SO4.8: 7 residues within 4Å: Chain C: H.230, N.233, L.260, R.300, H.306, R.315, R.388 10 PLIP interactions: 10 interactions with chain C Water bridges: C:H.230, C:H.306, C:H.306, C:R.315, C:D.363 Salt bridges: C:H.230, C:R.300, C:H.306, C:R.315, C:R.388 SO4.10: 6 residues within 4Å: Chain C: I.406, R.408 Chain D: N.233, A.234, R.300, R.307 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.234 Water bridges: D:R.300 Salt bridges: D:R.300, D:R.307, C:R.408 SO4.11: 6 residues within 4Å: Chain D: H.230, N.233, H.306, R.315, D.363, R.388 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.300 Water bridges: D:H.230 Salt bridges: D:H.230, D:H.306, D:R.315, D:R.388 SO4.13: 6 residues within 4Å: Chain E: N.233, A.234, R.300, R.307 Chain F: I.406, R.408 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain E Salt bridges: F:R.408, E:R.300, E:R.307 Hydrogen bonds: E:A.234 Water bridges: E:S.235, E:R.307, E:R.307 SO4.14: 7 residues within 4Å: Chain E: H.230, N.233, L.260, R.300, H.306, R.315, R.388 10 PLIP interactions: 10 interactions with chain E Water bridges: E:H.230, E:H.306, E:H.306, E:R.315, E:D.363 Salt bridges: E:H.230, E:R.300, E:H.306, E:R.315, E:R.388 SO4.16: 6 residues within 4Å: Chain E: I.406, R.408 Chain F: N.233, A.234, R.300, R.307 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:A.234 Water bridges: F:R.300 Salt bridges: F:R.300, F:R.307, E:R.408 SO4.17: 6 residues within 4Å: Chain F: H.230, N.233, H.306, R.315, D.363, R.388 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.300 Water bridges: F:H.230 Salt bridges: F:H.230, F:H.306, F:R.315, F:R.388

6 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 18 residues within 4Å: Chain A: T.107, T.109, R.110, H.111, T.112, M.113, I.114, H.115, Y.146, I.160, F.163, R.164, K.168, N.190 Chain C: I.181, Q.183, T.205, C.207 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:T.107, A:F.163 Hydrogen bonds: A:R.110, A:T.112, A:T.112, A:M.113, A:H.115, A:R.164, A:N.190, A:N.190, C:I.181, C:Q.183, C:T.205 Water bridges: A:E.159 Salt bridges: A:H.111, A:R.164, A:K.168, A:K.168 pi-Stacking: A:H.111 NAI.6: 16 residues within 4Å: Chain B: T.107, T.109, R.110, H.111, T.112, M.113, H.115, Y.146, D.148, I.160, F.163, R.164, K.168, N.190 Chain F: Q.183, C.207 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:T.107, B:F.163 Hydrogen bonds: B:T.112, B:T.112, B:M.113, B:M.113, B:H.115, B:Y.146, B:N.190 Water bridges: B:R.110, B:R.110, B:E.159, B:R.164, F:I.181 Salt bridges: B:H.111, B:R.164, B:K.168, B:K.168 pi-Stacking: B:H.111 pi-Cation interactions: B:H.111 NAI.9: 18 residues within 4Å: Chain C: T.107, T.109, R.110, H.111, T.112, M.113, I.114, H.115, Y.146, I.160, F.163, R.164, K.168, N.190 Chain E: I.181, Q.183, T.205, C.207 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:T.107, C:F.163 Hydrogen bonds: C:R.110, C:T.112, C:T.112, C:M.113, C:H.115, C:R.164, C:N.190, C:N.190, E:I.181, E:Q.183, E:T.205 Water bridges: C:E.159 Salt bridges: C:H.111, C:R.164, C:K.168, C:K.168 pi-Stacking: C:H.111 NAI.12: 16 residues within 4Å: Chain B: Q.183, C.207 Chain D: T.107, T.109, R.110, H.111, T.112, M.113, H.115, Y.146, D.148, I.160, F.163, R.164, K.168, N.190 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:T.107, D:F.163 Hydrogen bonds: D:T.112, D:T.112, D:M.113, D:M.113, D:H.115, D:Y.146, D:N.190 Water bridges: D:R.110, D:R.110, D:E.159, D:R.164, B:I.181 Salt bridges: D:H.111, D:R.164, D:K.168, D:K.168 pi-Stacking: D:H.111 pi-Cation interactions: D:H.111 NAI.15: 18 residues within 4Å: Chain A: I.181, Q.183, T.205, C.207 Chain E: T.107, T.109, R.110, H.111, T.112, M.113, I.114, H.115, Y.146, I.160, F.163, R.164, K.168, N.190 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:T.107, E:F.163 Hydrogen bonds: E:R.110, E:T.112, E:T.112, E:M.113, E:H.115, E:R.164, E:N.190, E:N.190, A:I.181, A:Q.183, A:T.205 Water bridges: E:E.159 Salt bridges: E:H.111, E:R.164, E:K.168, E:K.168 pi-Stacking: E:H.111 NAI.18: 16 residues within 4Å: Chain D: Q.183, C.207 Chain F: T.107, T.109, R.110, H.111, T.112, M.113, H.115, Y.146, D.148, I.160, F.163, R.164, K.168, N.190 20 PLIP interactions: 19 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:T.107, F:F.163 Hydrogen bonds: F:T.112, F:T.112, F:M.113, F:M.113, F:H.115, F:Y.146, F:N.190 Water bridges: F:R.110, F:R.110, F:E.159, F:R.164, D:I.181 Salt bridges: F:H.111, F:R.164, F:K.168, F:K.168 pi-Stacking: F:H.111 pi-Cation interactions: F:H.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurus, R. et al., Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases. Biochemistry (2003)

Release Date

2003-04-08

Peptides

Citrate synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Citrate synthase

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