SMTL ID : 3oyz.2 (1 other biounit)

Haloferax volcanii Malate Synthase Pyruvate/Acetyl-CoA Ternary Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-hexamer

Ligands

6 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 23 residues within 4Å: Chain A: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.191, A:P.231, A:I.235, A:A.363 Hydrogen bonds: A:T.16, A:T.16, A:R.84, A:R.84, A:L.259, A:D.388, A:D.388 Water bridges: A:R.236, A:R.236, A:T.260 Salt bridges: A:R.33, A:R.236, A:R.236 ACO.12: 23 residues within 4Å: Chain B: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.13 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.191, B:P.231, B:I.235, B:A.363 Hydrogen bonds: B:T.16, B:T.16, B:R.84, B:R.84, B:L.259, B:D.388, B:D.388 Water bridges: B:R.236, B:R.236, B:T.260 Salt bridges: B:R.33, B:R.236, B:R.236 ACO.23: 23 residues within 4Å: Chain C: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.24 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.191, C:P.231, C:I.235, C:A.363 Hydrogen bonds: C:T.16, C:T.16, C:R.84, C:R.84, C:L.259, C:D.388, C:D.388 Water bridges: C:R.236, C:R.236, C:T.260 Salt bridges: C:R.33, C:R.236, C:R.236 ACO.34: 23 residues within 4Å: Chain D: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.35 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:V.191, D:P.231, D:I.235, D:A.363 Hydrogen bonds: D:T.16, D:R.84, D:R.84, D:L.259, D:D.388 Water bridges: D:R.236, D:R.236, D:T.260, D:T.260 Salt bridges: D:R.33, D:R.236, D:R.236 ACO.45: 23 residues within 4Å: Chain E: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.46 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:V.191, E:P.231, E:I.235, E:A.363 Hydrogen bonds: E:T.16, E:R.84, E:R.84, E:L.259, E:D.388 Water bridges: E:R.236, E:R.236, E:T.260, E:T.260 Salt bridges: E:R.33, E:R.236, E:R.236 ACO.56: 23 residues within 4Å: Chain F: F.15, T.16, S.17, P.18, M.30, R.33, A.34, D.49, D.52, A.53, R.84, V.191, P.231, I.235, R.236, W.257, L.259, T.260, P.261, A.363, M.386, D.388 Ligands: PYR.57 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:V.191, F:P.231, F:I.235, F:A.363 Hydrogen bonds: F:T.16, F:R.84, F:R.84, F:L.259, F:D.388 Water bridges: F:R.236, F:R.236, F:T.260, F:T.260 Salt bridges: F:R.33, F:R.236, F:R.236

6 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 10 residues within 4Å: Chain A: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.1, MG.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.231, A:W.257 Hydrogen bonds: A:R.84, A:R.84, A:V.191, A:D.192 PYR.13: 10 residues within 4Å: Chain B: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.12, MG.14 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.231, B:W.257 Hydrogen bonds: B:R.84, B:R.84, B:V.191, B:D.192 PYR.24: 10 residues within 4Å: Chain C: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.23, MG.25 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.231, C:W.257 Hydrogen bonds: C:R.84, C:R.84, C:V.191, C:D.192 PYR.35: 10 residues within 4Å: Chain D: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.34, MG.36 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:P.231, D:W.257 Hydrogen bonds: D:R.84, D:R.84, D:V.191, D:D.192 PYR.46: 10 residues within 4Å: Chain E: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.45, MG.47 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:P.231, E:W.257 Hydrogen bonds: E:R.84, E:R.84, E:V.191, E:D.192 PYR.57: 10 residues within 4Å: Chain F: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: ACO.56, MG.58 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:P.231, F:W.257 Hydrogen bonds: F:R.84, F:R.84, F:V.191, F:D.192

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.158, D.192 Ligands: PYR.2 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:E.158, A:D.192, H2O.2, H2O.3, PYR.2 MG.14: 3 residues within 4Å: Chain B: E.158, D.192 Ligands: PYR.13 5 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:E.158, B:D.192, H2O.9, H2O.10, PYR.13 MG.25: 3 residues within 4Å: Chain C: E.158, D.192 Ligands: PYR.24 5 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:E.158, C:D.192, H2O.15, H2O.16, PYR.24 MG.36: 3 residues within 4Å: Chain D: E.158, D.192 Ligands: PYR.35 5 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:E.158, D:D.192, H2O.22, H2O.23, PYR.35 MG.47: 3 residues within 4Å: Chain E: E.158, D.192 Ligands: PYR.46 5 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:E.158, E:D.192, H2O.29, H2O.30, PYR.46 MG.58: 3 residues within 4Å: Chain F: E.158, D.192 Ligands: PYR.57 5 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:E.158, F:D.192, H2O.36, H2O.37, PYR.57

18 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.5: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.10 Ligand excluded by PLIP K.6: 3 residues within 4Å: Chain A: P.176, N.178, N.179 Ligand excluded by PLIP K.15: 4 residues within 4Å: Chain B: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.16: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.21 Ligand excluded by PLIP K.17: 3 residues within 4Å: Chain B: P.176, N.178, N.179 Ligand excluded by PLIP K.26: 4 residues within 4Å: Chain C: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.27: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.32 Ligand excluded by PLIP K.28: 3 residues within 4Å: Chain C: P.176, N.178, N.179 Ligand excluded by PLIP K.37: 4 residues within 4Å: Chain D: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.38: 5 residues within 4Å: Chain D: S.217, S.221, G.252 Chain E: M.197 Ligands: CL.43 Ligand excluded by PLIP K.39: 3 residues within 4Å: Chain D: P.176, N.178, N.179 Ligand excluded by PLIP K.48: 4 residues within 4Å: Chain E: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.49: 5 residues within 4Å: Chain E: S.217, S.221, G.252 Chain F: M.197 Ligands: CL.54 Ligand excluded by PLIP K.50: 3 residues within 4Å: Chain E: P.176, N.178, N.179 Ligand excluded by PLIP K.59: 4 residues within 4Å: Chain F: M.173, K.175, N.178, E.181 Ligand excluded by PLIP K.60: 5 residues within 4Å: Chain D: M.197 Chain F: S.217, S.221, G.252 Ligands: CL.65 Ligand excluded by PLIP K.61: 3 residues within 4Å: Chain F: P.176, N.178, N.179 Ligand excluded by PLIP

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: R.170 Chain B: G.126, I.127, A.165 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: V.226, A.227, G.252 Chain B: R.198 Ligands: K.5 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain B: R.170 Chain C: G.126, I.127, A.165 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain B: V.226, A.227, G.252 Chain C: R.198 Ligands: K.16 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain A: G.126, I.127, A.165 Chain C: R.170 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.32: 5 residues within 4Å: Chain A: R.198 Chain C: V.226, A.227, G.252 Ligands: K.27 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain D: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain D: R.170 Chain E: G.126, I.127, A.165 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.43: 5 residues within 4Å: Chain D: V.226, A.227, G.252 Chain E: R.198 Ligands: K.38 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain E: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain E: R.170 Chain F: G.126, I.127, A.165 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain E: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain E: V.226, A.227, G.252 Chain F: R.198 Ligands: K.49 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain F: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain D: G.126, I.127, A.165 Chain F: R.170 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain F: N.50, M.85, V.86, H.101 Ligand excluded by PLIP CL.65: 5 residues within 4Å: Chain D: R.198 Chain F: V.226, A.227, G.252 Ligands: K.60 Ligand excluded by PLIP

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.11: 8 residues within 4Å: Chain A: N.215, R.218 Chain B: N.215, R.218 Chain C: N.215, R.218 Ligands: PO4.22, PO4.33 13 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:N.215, B:N.215 Water bridges: C:N.215, C:N.215, C:R.218, A:N.215, A:N.215, A:R.218, B:N.215, B:R.218 Salt bridges: C:R.218, A:R.218, B:R.218 PO4.22: 8 residues within 4Å: Chain A: N.215, R.218 Chain B: N.215, R.218 Chain C: N.215, R.218 Ligands: PO4.11, PO4.33 13 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: C:N.215, A:N.215 Water bridges: C:N.215, C:R.218, A:N.215, A:N.215, A:R.218, B:N.215, B:N.215, B:R.218 Salt bridges: C:R.218, A:R.218, B:R.218 PO4.33: 8 residues within 4Å: Chain A: N.215, R.218 Chain B: N.215, R.218 Chain C: N.215, R.218 Ligands: PO4.11, PO4.22 13 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A, 5 interactions with chain B Water bridges: C:N.215, C:N.215, C:R.218, A:N.215, A:R.218, B:N.215, B:N.215, B:R.218 Salt bridges: C:R.218, A:R.218, B:R.218 Hydrogen bonds: A:N.215, B:N.215 PO4.44: 8 residues within 4Å: Chain D: N.215, R.218 Chain E: N.215, R.218 Chain F: N.215, R.218 Ligands: PO4.55, PO4.66 13 PLIP interactions: 4 interactions with chain E, 4 interactions with chain D, 5 interactions with chain F Hydrogen bonds: E:N.215, F:N.215 Water bridges: E:N.215, E:R.218, D:N.215, D:N.215, D:R.218, F:N.215, F:N.215, F:R.218 Salt bridges: E:R.218, D:R.218, F:R.218 PO4.55: 8 residues within 4Å: Chain D: N.215, R.218 Chain E: N.215, R.218 Chain F: N.215, R.218 Ligands: PO4.44, PO4.66 13 PLIP interactions: 4 interactions with chain E, 5 interactions with chain D, 4 interactions with chain F Water bridges: E:N.215, E:N.215, E:R.218, D:N.215, D:N.215, D:R.218, F:N.215, F:R.218 Salt bridges: E:R.218, D:R.218, F:R.218 Hydrogen bonds: D:N.215, F:N.215 PO4.66: 8 residues within 4Å: Chain D: N.215, R.218 Chain E: N.215, R.218 Chain F: N.215, R.218 Ligands: PO4.44, PO4.55 13 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D, 4 interactions with chain F Hydrogen bonds: E:N.215, D:N.215 Water bridges: E:N.215, E:N.215, E:R.218, D:N.215, D:R.218, F:N.215, F:N.215, F:R.218 Salt bridges: E:R.218, D:R.218, F:R.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bracken, C.D. et al., Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. Bmc Struct.Biol. (2011)

Release Date

2011-06-01

Peptides

Malate Synthase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Malate Synthase

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