SMTL ID : 3oyz.1 (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-trimer

Ligands

3 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

3 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

3 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

9 x K: POTASSIUM ION(Non-covalent)

K.4: 4 residues within 4Å: Chain A: M.173, K.175, N.178, E.181 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.173, A:K.175, A:N.178, A:E.181, H2O.2 K.5: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:M.197, A:S.217, A:S.221, A:G.252 K.6: 3 residues within 4Å: Chain A: P.176, N.178, N.179 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:P.176, A:N.178 K.15: 4 residues within 4Å: Chain B: M.173, K.175, N.178, E.181 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.173, B:K.175, B:N.178, B:E.181, H2O.9 K.16: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.21 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:S.217, B:S.221, B:G.252, C:M.197 K.17: 3 residues within 4Å: Chain B: P.176, N.178, N.179 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:P.176, B:N.178 K.26: 4 residues within 4Å: Chain C: M.173, K.175, N.178, E.181 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.173, C:K.175, C:N.178, C:E.181, H2O.16 K.27: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.32 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Metal complexes: A:M.197, C:S.217, C:S.221, C:G.252 K.28: 3 residues within 4Å: Chain C: P.176, N.178, N.179 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:P.176, C:N.178

12 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

3 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: 4 interactions with chain A, 4 interactions with chain B, 5 interactions with chain C Water bridges: A:N.215, A:N.215, A:R.218, B:N.215, B:R.218, C:N.215, C:N.215, C:R.218 Salt bridges: A:R.218, B:R.218, C:R.218 Hydrogen bonds: B:N.215, C:N.215 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, 4 interactions with chain B, 5 interactions with chain A Hydrogen bonds: C:N.215, A:N.215 Water bridges: C:N.215, C:R.218, B:N.215, B:N.215, B:R.218, A:N.215, A:N.215, A:R.218 Salt bridges: C:R.218, B:R.218, A: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, 5 interactions with chain B, 4 interactions with chain A Water bridges: C:N.215, C:N.215, C:R.218, B:N.215, B:N.215, B:R.218, A:N.215, A:R.218 Salt bridges: C:R.218, B:R.218, A:R.218 Hydrogen bonds: B:N.215, A:N.215

Links

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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: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Malate Synthase

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