SMTL ID : 5tao.2 (1 other biounit)

Haloferax volcanii Malate Synthase Lead(II) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.9, K.11 No protein-ligand interaction detected (PLIP) ACT.17: 8 residues within 4Å: Chain B: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.25, K.27 No protein-ligand interaction detected (PLIP) ACT.33: 8 residues within 4Å: Chain C: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.41, K.43 No protein-ligand interaction detected (PLIP)

9 x GLV: GLYOXYLIC ACID(Non-covalent)

GLV.2: 8 residues within 4Å: Chain A: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.158, A:V.191, A:D.192 Salt bridges: A:R.84 GLV.3: 6 residues within 4Å: Chain A: R.89, D.90, E.161, D.196 Ligands: PB.5, PB.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:S.221, A:R.89 Salt bridges: A:R.89 GLV.4: 6 residues within 4Å: Chain A: E.51, D.52, H.88, E.123, D.192 Ligands: PB.6 No protein-ligand interaction detected (PLIP) GLV.18: 8 residues within 4Å: Chain B: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.158, B:V.191, B:D.192 Salt bridges: B:R.84 GLV.19: 6 residues within 4Å: Chain B: R.89, D.90, E.161, D.196 Ligands: PB.21, PB.23 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.221, B:R.89 Salt bridges: B:R.89 GLV.20: 6 residues within 4Å: Chain B: E.51, D.52, H.88, E.123, D.192 Ligands: PB.22 No protein-ligand interaction detected (PLIP) GLV.34: 8 residues within 4Å: Chain C: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.38 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.158, C:V.191, C:D.192 Salt bridges: C:R.84 GLV.35: 6 residues within 4Å: Chain C: R.89, D.90, E.161, D.196 Ligands: PB.37, PB.39 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:S.221, C:R.89 Salt bridges: C:R.89 GLV.36: 6 residues within 4Å: Chain C: E.51, D.52, H.88, E.123, D.192 Ligands: PB.38 No protein-ligand interaction detected (PLIP)

12 x PB: LEAD (II) ION(Non-covalent)

PB.5: 4 residues within 4Å: Chain A: E.161, D.196 Chain C: S.221 Ligands: GLV.3 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.161, A:E.161, A:D.196, C:S.221, H2O.7 PB.6: 7 residues within 4Å: Chain A: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.2, GLV.4 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.51, A:D.52, A:E.158, A:E.158, A:D.192 PB.7: 3 residues within 4Å: Chain A: D.90, E.161 Ligands: GLV.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.90 PB.8: 3 residues within 4Å: Chain A: D.344, D.348, R.427 No protein-ligand interaction detected (PLIP) PB.21: 4 residues within 4Å: Chain A: S.221 Chain B: E.161, D.196 Ligands: GLV.19 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:S.221, B:E.161, B:E.161, B:D.196, H2O.17 PB.22: 7 residues within 4Å: Chain B: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.18, GLV.20 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.51, B:D.52, B:E.158, B:E.158, B:D.192 PB.23: 3 residues within 4Å: Chain B: D.90, E.161 Ligands: GLV.19 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.90 PB.24: 3 residues within 4Å: Chain B: D.344, D.348, R.427 No protein-ligand interaction detected (PLIP) PB.37: 4 residues within 4Å: Chain B: S.221 Chain C: E.161, D.196 Ligands: GLV.35 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:S.221, C:E.161, C:E.161, C:D.196, H2O.27 PB.38: 7 residues within 4Å: Chain C: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.34, GLV.36 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.51, C:D.52, C:E.158, C:E.158, C:D.192 PB.39: 3 residues within 4Å: Chain C: D.90, E.161 Ligands: GLV.35 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.90 PB.40: 3 residues within 4Å: Chain C: D.344, D.348, R.427 No protein-ligand interaction detected (PLIP)

9 x K: POTASSIUM ION(Non-covalent)

K.9: 6 residues within 4Å: Chain A: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.173, A:K.175, A:N.178, A:E.181, A:E.181 K.10: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.14 5 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:M.197, A:S.217, A:S.221, A:G.252, H2O.1 K.11: 4 residues within 4Å: Chain A: P.176, N.178, N.179 Ligands: ACT.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:P.176, A:N.178, ACT.1 K.25: 6 residues within 4Å: Chain B: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.17 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:M.173, B:K.175, B:N.178, B:E.181, B:E.181 K.26: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.30 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:S.217, B:S.221, B:G.252, C:M.197, H2O.10 K.27: 4 residues within 4Å: Chain B: P.176, N.178, N.179 Ligands: ACT.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:P.176, B:N.178, ACT.17 K.41: 6 residues within 4Å: Chain C: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.33 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:M.173, C:K.175, C:N.178, C:E.181, C:E.181 K.42: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.46 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:S.217, C:S.221, C:G.252, A:M.197, H2O.20 K.43: 4 residues within 4Å: Chain C: P.176, N.178, N.179 Ligands: ACT.33 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:P.176, C:N.178, ACT.33

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

CL.12: 4 residues within 4Å: Chain A: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.29, CL.45 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: V.226, A.227, G.252 Chain B: R.198 Ligands: K.10 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: G.125, G.126 Chain C: R.170 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.13, CL.45 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: V.226, A.227, G.252 Chain C: R.198 Ligands: K.26 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain A: R.170 Chain B: G.125, G.126 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain C: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.45: 5 residues within 4Å: Chain A: R.218 Chain B: R.218 Chain C: R.218 Ligands: CL.13, CL.29 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain A: R.198 Chain C: V.226, A.227, G.252 Ligands: K.42 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain B: R.170 Chain C: G.125, G.126 Ligand excluded by PLIP

3 x NA: SODIUM ION(Non-functional Binders)

NA.16: 2 residues within 4Å: Chain A: N.408 Chain C: P.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.78 NA.32: 2 residues within 4Å: Chain A: P.78 Chain B: N.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.408 NA.48: 2 residues within 4Å: Chain B: P.78 Chain C: N.408 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, M.J. et al., X-ray analysis of Lead(II) binding to Haloferax volcanii Malate Synthase. The Journal of the Utah Academy (2016)

Release Date

2016-11-09

Peptides

Malate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Malate synthase

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