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

Haloferax volcanii Malate Synthase Native at 3mM Glyoxylate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

6 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.1: 9 residues within 4Å: Chain A: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.84, A:R.84, A:V.191, A:D.192, A:D.192 GLV.11: 9 residues within 4Å: Chain B: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.84, B:R.84, B:V.191, B:D.192, B:D.192 GLV.21: 9 residues within 4Å: Chain C: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.22 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.84, C:R.84, C:V.191, C:D.192, C:D.192 GLV.31: 9 residues within 4Å: Chain D: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.32 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.84, D:R.84, D:E.158, D:V.191, D:D.192, D:D.192 Water bridges: D:D.52, D:D.52 GLV.41: 9 residues within 4Å: Chain E: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.42 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:R.84, E:R.84, E:E.158, E:V.191, E:D.192, E:D.192 Water bridges: E:D.52, E:D.52 GLV.51: 9 residues within 4Å: Chain F: R.84, E.158, G.189, E.190, V.191, D.192, P.231, W.257 Ligands: MG.52 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:R.84, F:R.84, F:E.158, F:V.191, F:D.192, F:D.192 Water bridges: F:D.52, F:D.52

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.52, E.158, D.192 Ligands: GLV.1, K.9 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:E.158, A:D.192, H2O.2 MG.12: 5 residues within 4Å: Chain B: D.52, E.158, D.192 Ligands: GLV.11, K.19 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.52, B:E.158, B:D.192, H2O.5 MG.22: 5 residues within 4Å: Chain C: D.52, E.158, D.192 Ligands: GLV.21, K.29 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.52, C:E.158, C:D.192, H2O.8 MG.32: 5 residues within 4Å: Chain D: D.52, E.158, D.192 Ligands: GLV.31, K.39 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.52, D:E.158, D:D.192, H2O.10 MG.42: 5 residues within 4Å: Chain E: D.52, E.158, D.192 Ligands: GLV.41, K.49 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.52, E:E.158, E:D.192, H2O.13 MG.52: 5 residues within 4Å: Chain F: D.52, E.158, D.192 Ligands: GLV.51, K.59 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.52, F:E.158, F:D.192, H2O.16

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

CL.3: 6 residues within 4Å: Chain A: R.4, V.226, A.227, G.252 Chain B: R.198 Ligands: K.8 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: P.207, A.208 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.16, CL.26 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: R.4, V.226, A.227, G.252 Chain C: R.198 Ligands: K.18 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: P.207, A.208 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.6, CL.26 Ligand excluded by PLIP CL.23: 6 residues within 4Å: Chain A: R.198 Chain C: R.4, V.226, A.227, G.252 Ligands: K.28 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain C: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain C: P.207, A.208 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.6, CL.16 Ligand excluded by PLIP CL.33: 6 residues within 4Å: Chain D: R.4, V.226, A.227, G.252 Chain E: R.198 Ligands: K.38 Ligand excluded by PLIP CL.34: 5 residues within 4Å: Chain D: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain D: P.207, A.208 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.46, CL.56 Ligand excluded by PLIP CL.43: 6 residues within 4Å: Chain E: R.4, V.226, A.227, G.252 Chain F: R.198 Ligands: K.48 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain E: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain E: P.207, A.208 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.36, CL.56 Ligand excluded by PLIP CL.53: 6 residues within 4Å: Chain D: R.198 Chain F: R.4, V.226, A.227, G.252 Ligands: K.58 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain F: R.89, D.90, S.91, P.92, R.95 Ligand excluded by PLIP CL.55: 2 residues within 4Å: Chain F: P.207, A.208 Ligand excluded by PLIP CL.56: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.36, CL.46 Ligand excluded by PLIP

24 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.8: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.3 Ligand excluded by PLIP K.9: 5 residues within 4Å: Chain A: E.51, D.52, E.123, D.192 Ligands: MG.2 Ligand excluded by PLIP K.10: 3 residues within 4Å: Chain A: P.176, N.178, N.179 Ligand excluded by PLIP K.17: 5 residues within 4Å: Chain B: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.18: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.13 Ligand excluded by PLIP K.19: 5 residues within 4Å: Chain B: E.51, D.52, E.123, D.192 Ligands: MG.12 Ligand excluded by PLIP K.20: 3 residues within 4Å: Chain B: P.176, N.178, N.179 Ligand excluded by PLIP K.27: 5 residues within 4Å: Chain C: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.28: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.23 Ligand excluded by PLIP K.29: 5 residues within 4Å: Chain C: E.51, D.52, E.123, D.192 Ligands: MG.22 Ligand excluded by PLIP K.30: 3 residues within 4Å: Chain C: P.176, N.178, N.179 Ligand excluded by PLIP K.37: 5 residues within 4Å: Chain D: M.173, G.174, 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.33 Ligand excluded by PLIP K.39: 5 residues within 4Å: Chain D: E.51, D.52, E.123, D.192 Ligands: MG.32 Ligand excluded by PLIP K.40: 3 residues within 4Å: Chain D: P.176, N.178, N.179 Ligand excluded by PLIP K.47: 5 residues within 4Å: Chain E: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.48: 5 residues within 4Å: Chain E: S.217, S.221, G.252 Chain F: M.197 Ligands: CL.43 Ligand excluded by PLIP K.49: 5 residues within 4Å: Chain E: E.51, D.52, E.123, D.192 Ligands: MG.42 Ligand excluded by PLIP K.50: 3 residues within 4Å: Chain E: P.176, N.178, N.179 Ligand excluded by PLIP K.57: 5 residues within 4Å: Chain F: M.173, G.174, K.175, N.178, E.181 Ligand excluded by PLIP K.58: 5 residues within 4Å: Chain D: M.197 Chain F: S.217, S.221, G.252 Ligands: CL.53 Ligand excluded by PLIP K.59: 5 residues within 4Å: Chain F: E.51, D.52, E.123, D.192 Ligands: MG.52 Ligand excluded by PLIP K.60: 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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