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

Haloferax volcanii Malate Synthase Magnesium/Glyoxylate Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-hexamer

Ligands

12 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.1: 10 residues within 4Å: Chain A: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.2, MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:V.191, A:D.192 GLV.2: 5 residues within 4Å: Chain A: R.84, W.257, D.388, A.390 Ligands: GLV.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.84 Salt bridges: A:R.84 GLV.12: 10 residues within 4Å: Chain B: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.13, MG.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.84, B:R.84, B:V.191, B:D.192 GLV.13: 5 residues within 4Å: Chain B: R.84, W.257, D.388, A.390 Ligands: GLV.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.84 Salt bridges: B:R.84 GLV.23: 10 residues within 4Å: Chain C: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.24, MG.25 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.84, C:R.84, C:V.191, C:D.192 GLV.24: 5 residues within 4Å: Chain C: R.84, W.257, D.388, A.390 Ligands: GLV.23 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.84 Salt bridges: C:R.84 GLV.34: 10 residues within 4Å: Chain D: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.35, MG.36 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.84, D:R.84, D:E.158, D:V.191, D:D.192 GLV.35: 5 residues within 4Å: Chain D: R.84, W.257, D.388, A.390 Ligands: GLV.34 2 PLIP interactions: 2 interactions with chain D Water bridges: D:R.84 Salt bridges: D:R.84 GLV.45: 10 residues within 4Å: Chain E: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.46, MG.47 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.84, E:R.84, E:E.158, E:V.191, E:D.192 GLV.46: 5 residues within 4Å: Chain E: R.84, W.257, D.388, A.390 Ligands: GLV.45 2 PLIP interactions: 2 interactions with chain E Water bridges: E:R.84 Salt bridges: E:R.84 GLV.56: 10 residues within 4Å: Chain F: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: GLV.57, MG.58 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.84, F:R.84, F:E.158, F:V.191, F:D.192 GLV.57: 5 residues within 4Å: Chain F: R.84, W.257, D.388, A.390 Ligands: GLV.56 2 PLIP interactions: 2 interactions with chain F Water bridges: F:R.84 Salt bridges: F:R.84

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: R.84, E.158, D.192 Ligands: GLV.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.158, A:D.192, H2O.1, H2O.1 MG.14: 4 residues within 4Å: Chain B: R.84, E.158, D.192 Ligands: GLV.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.158, B:D.192, H2O.6, H2O.6 MG.25: 4 residues within 4Å: Chain C: R.84, E.158, D.192 Ligands: GLV.23 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.158, C:D.192, H2O.11, H2O.11 MG.36: 4 residues within 4Å: Chain D: R.84, E.158, D.192 Ligands: GLV.34 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.158, D:D.192, H2O.16, H2O.16 MG.47: 4 residues within 4Å: Chain E: R.84, E.158, D.192 Ligands: GLV.45 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.158, E:D.192, H2O.21, H2O.21 MG.58: 4 residues within 4Å: Chain F: R.84, E.158, D.192 Ligands: GLV.56 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.158, F:D.192, H2O.26, H2O.27

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

CL.4: 5 residues within 4Å: Chain A: V.226, A.227, G.252 Chain B: R.198 Ligands: K.9 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.17, CL.28 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.207, A.208 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: G.126, I.127, A.165 Chain C: R.170 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: V.226, A.227, G.252 Chain C: R.198 Ligands: K.20 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain B: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.6, CL.28 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: P.207, A.208 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: R.170 Chain B: G.126, I.127, A.165 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: R.198 Chain C: V.226, A.227, G.252 Ligands: K.31 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain C: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.28: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.6, CL.17 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: P.207, A.208 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain B: R.170 Chain C: G.126, I.127, A.165 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain D: V.226, A.227, G.252 Chain E: R.198 Ligands: K.42 Ligand excluded by PLIP CL.38: 5 residues within 4Å: Chain D: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.39: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.50, CL.61 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain D: P.207, A.208 Ligand excluded by PLIP CL.41: 4 residues within 4Å: Chain D: G.126, I.127, A.165 Chain F: R.170 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain E: V.226, A.227, G.252 Chain F: R.198 Ligands: K.53 Ligand excluded by PLIP CL.49: 5 residues within 4Å: Chain E: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.50: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.39, CL.61 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain E: P.207, A.208 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain D: R.170 Chain E: G.126, I.127, A.165 Ligand excluded by PLIP CL.59: 5 residues within 4Å: Chain D: R.198 Chain F: V.226, A.227, G.252 Ligands: K.64 Ligand excluded by PLIP CL.60: 5 residues within 4Å: Chain F: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.61: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.39, CL.50 Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain F: P.207, A.208 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain E: R.170 Chain F: G.126, I.127, A.165 Ligand excluded by PLIP

18 x K: POTASSIUM ION(Non-covalent)

K.9: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.4 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain A: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.11: 3 residues within 4Å: Chain A: P.176, N.178, N.179 Ligand excluded by PLIP K.20: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.15 Ligand excluded by PLIP K.21: 5 residues within 4Å: Chain B: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.22: 3 residues within 4Å: Chain B: P.176, N.178, N.179 Ligand excluded by PLIP K.31: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.26 Ligand excluded by PLIP K.32: 5 residues within 4Å: Chain C: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.33: 3 residues within 4Å: Chain C: P.176, N.178, N.179 Ligand excluded by PLIP K.42: 5 residues within 4Å: Chain D: S.217, S.221, G.252 Chain E: M.197 Ligands: CL.37 Ligand excluded by PLIP K.43: 5 residues within 4Å: Chain D: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.44: 3 residues within 4Å: Chain D: P.176, N.178, N.179 Ligand excluded by PLIP K.53: 5 residues within 4Å: Chain E: S.217, S.221, G.252 Chain F: M.197 Ligands: CL.48 Ligand excluded by PLIP K.54: 5 residues within 4Å: Chain E: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.55: 3 residues within 4Å: Chain E: P.176, N.178, N.179 Ligand excluded by PLIP K.64: 5 residues within 4Å: Chain D: M.197 Chain F: S.217, S.221, G.252 Ligands: CL.59 Ligand excluded by PLIP K.65: 5 residues within 4Å: Chain F: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.66: 3 residues within 4Å: Chain F: P.176, N.178, N.179 Ligand excluded by PLIP

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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