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

Haloferax volcanii Malate Synthase Lead(II) complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.174 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.174 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 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.174 ACT.49: 8 residues within 4Å: Chain D: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.57, K.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.174 ACT.65: 8 residues within 4Å: Chain E: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.73, K.75 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.174 ACT.81: 8 residues within 4Å: Chain F: G.174, K.175, P.176, N.178, N.179, E.181 Ligands: K.89, K.91 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.174

18 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 Ligand excluded by PLIP GLV.3: 6 residues within 4Å: Chain A: R.89, D.90, E.161, D.196 Ligands: PB.5, PB.7 Ligand excluded by PLIP GLV.4: 6 residues within 4Å: Chain A: E.51, D.52, H.88, E.123, D.192 Ligands: PB.6 Ligand excluded by 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 Ligand excluded by PLIP GLV.19: 6 residues within 4Å: Chain B: R.89, D.90, E.161, D.196 Ligands: PB.21, PB.23 Ligand excluded by PLIP GLV.20: 6 residues within 4Å: Chain B: E.51, D.52, H.88, E.123, D.192 Ligands: PB.22 Ligand excluded by 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 Ligand excluded by PLIP GLV.35: 6 residues within 4Å: Chain C: R.89, D.90, E.161, D.196 Ligands: PB.37, PB.39 Ligand excluded by PLIP GLV.36: 6 residues within 4Å: Chain C: E.51, D.52, H.88, E.123, D.192 Ligands: PB.38 Ligand excluded by PLIP GLV.50: 8 residues within 4Å: Chain D: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.54 Ligand excluded by PLIP GLV.51: 6 residues within 4Å: Chain D: R.89, D.90, E.161, D.196 Ligands: PB.53, PB.55 Ligand excluded by PLIP GLV.52: 6 residues within 4Å: Chain D: E.51, D.52, H.88, E.123, D.192 Ligands: PB.54 Ligand excluded by PLIP GLV.66: 8 residues within 4Å: Chain E: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.70 Ligand excluded by PLIP GLV.67: 6 residues within 4Å: Chain E: R.89, D.90, E.161, D.196 Ligands: PB.69, PB.71 Ligand excluded by PLIP GLV.68: 6 residues within 4Å: Chain E: E.51, D.52, H.88, E.123, D.192 Ligands: PB.70 Ligand excluded by PLIP GLV.82: 8 residues within 4Å: Chain F: D.52, R.84, E.158, G.189, V.191, D.192, W.257 Ligands: PB.86 Ligand excluded by PLIP GLV.83: 6 residues within 4Å: Chain F: R.89, D.90, E.161, D.196 Ligands: PB.85, PB.87 Ligand excluded by PLIP GLV.84: 6 residues within 4Å: Chain F: E.51, D.52, H.88, E.123, D.192 Ligands: PB.86 Ligand excluded by PLIP

24 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 Ligand excluded by PLIP PB.6: 7 residues within 4Å: Chain A: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.2, GLV.4 Ligand excluded by PLIP PB.7: 3 residues within 4Å: Chain A: D.90, E.161 Ligands: GLV.3 Ligand excluded by PLIP PB.8: 3 residues within 4Å: Chain A: D.344, D.348, R.427 Ligand excluded by PLIP PB.21: 4 residues within 4Å: Chain A: S.221 Chain B: E.161, D.196 Ligands: GLV.19 Ligand excluded by PLIP PB.22: 7 residues within 4Å: Chain B: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.18, GLV.20 Ligand excluded by PLIP PB.23: 3 residues within 4Å: Chain B: D.90, E.161 Ligands: GLV.19 Ligand excluded by PLIP PB.24: 3 residues within 4Å: Chain B: D.344, D.348, R.427 Ligand excluded by PLIP PB.37: 4 residues within 4Å: Chain B: S.221 Chain C: E.161, D.196 Ligands: GLV.35 Ligand excluded by PLIP PB.38: 7 residues within 4Å: Chain C: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.34, GLV.36 Ligand excluded by PLIP PB.39: 3 residues within 4Å: Chain C: D.90, E.161 Ligands: GLV.35 Ligand excluded by PLIP PB.40: 3 residues within 4Å: Chain C: D.344, D.348, R.427 Ligand excluded by PLIP PB.53: 4 residues within 4Å: Chain D: E.161, D.196 Chain F: S.221 Ligands: GLV.51 Ligand excluded by PLIP PB.54: 7 residues within 4Å: Chain D: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.50, GLV.52 Ligand excluded by PLIP PB.55: 3 residues within 4Å: Chain D: D.90, E.161 Ligands: GLV.51 Ligand excluded by PLIP PB.56: 3 residues within 4Å: Chain D: D.344, D.348, R.427 Ligand excluded by PLIP PB.69: 4 residues within 4Å: Chain D: S.221 Chain E: E.161, D.196 Ligands: GLV.67 Ligand excluded by PLIP PB.70: 7 residues within 4Å: Chain E: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.66, GLV.68 Ligand excluded by PLIP PB.71: 3 residues within 4Å: Chain E: D.90, E.161 Ligands: GLV.67 Ligand excluded by PLIP PB.72: 3 residues within 4Å: Chain E: D.344, D.348, R.427 Ligand excluded by PLIP PB.85: 4 residues within 4Å: Chain E: S.221 Chain F: E.161, D.196 Ligands: GLV.83 Ligand excluded by PLIP PB.86: 7 residues within 4Å: Chain F: E.51, D.52, E.123, E.158, D.192 Ligands: GLV.82, GLV.84 Ligand excluded by PLIP PB.87: 3 residues within 4Å: Chain F: D.90, E.161 Ligands: GLV.83 Ligand excluded by PLIP PB.88: 3 residues within 4Å: Chain F: D.344, D.348, R.427 Ligand excluded by PLIP

18 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 Ligand excluded by PLIP K.10: 5 residues within 4Å: Chain A: S.217, S.221, G.252 Chain B: M.197 Ligands: CL.14 Ligand excluded by PLIP K.11: 4 residues within 4Å: Chain A: P.176, N.178, N.179 Ligands: ACT.1 Ligand excluded by PLIP K.25: 6 residues within 4Å: Chain B: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.17 Ligand excluded by PLIP K.26: 5 residues within 4Å: Chain B: S.217, S.221, G.252 Chain C: M.197 Ligands: CL.30 Ligand excluded by PLIP K.27: 4 residues within 4Å: Chain B: P.176, N.178, N.179 Ligands: ACT.17 Ligand excluded by PLIP K.41: 6 residues within 4Å: Chain C: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.33 Ligand excluded by PLIP K.42: 5 residues within 4Å: Chain A: M.197 Chain C: S.217, S.221, G.252 Ligands: CL.46 Ligand excluded by PLIP K.43: 4 residues within 4Å: Chain C: P.176, N.178, N.179 Ligands: ACT.33 Ligand excluded by PLIP K.57: 6 residues within 4Å: Chain D: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.49 Ligand excluded by PLIP K.58: 5 residues within 4Å: Chain D: S.217, S.221, G.252 Chain E: M.197 Ligands: CL.62 Ligand excluded by PLIP K.59: 4 residues within 4Å: Chain D: P.176, N.178, N.179 Ligands: ACT.49 Ligand excluded by PLIP K.73: 6 residues within 4Å: Chain E: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.65 Ligand excluded by PLIP K.74: 5 residues within 4Å: Chain E: S.217, S.221, G.252 Chain F: M.197 Ligands: CL.78 Ligand excluded by PLIP K.75: 4 residues within 4Å: Chain E: P.176, N.178, N.179 Ligands: ACT.65 Ligand excluded by PLIP K.89: 6 residues within 4Å: Chain F: M.173, G.174, K.175, N.178, E.181 Ligands: ACT.81 Ligand excluded by PLIP K.90: 5 residues within 4Å: Chain D: M.197 Chain F: S.217, S.221, G.252 Ligands: CL.94 Ligand excluded by PLIP K.91: 4 residues within 4Å: Chain F: P.176, N.178, N.179 Ligands: ACT.81 Ligand excluded by PLIP

24 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: 4 residues within 4Å: Chain A: G.125, G.126 Chain C: R.170 Chain E: T.177 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: 4 residues within 4Å: Chain A: R.170 Chain B: G.125, G.126 Chain D: T.177 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: 4 residues within 4Å: Chain B: R.170 Chain C: G.125, G.126 Chain F: T.177 Ligand excluded by PLIP CL.60: 4 residues within 4Å: Chain D: R.89, D.90, 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.77, CL.93 Ligand excluded by PLIP CL.62: 5 residues within 4Å: Chain D: V.226, A.227, G.252 Chain E: R.198 Ligands: K.58 Ligand excluded by PLIP CL.63: 4 residues within 4Å: Chain B: T.177 Chain D: G.125, G.126 Chain F: R.170 Ligand excluded by PLIP CL.76: 4 residues within 4Å: Chain E: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.77: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.61, CL.93 Ligand excluded by PLIP CL.78: 5 residues within 4Å: Chain E: V.226, A.227, G.252 Chain F: R.198 Ligands: K.74 Ligand excluded by PLIP CL.79: 4 residues within 4Å: Chain A: T.177 Chain D: R.170 Chain E: G.125, G.126 Ligand excluded by PLIP CL.92: 4 residues within 4Å: Chain F: R.89, D.90, P.92, R.95 Ligand excluded by PLIP CL.93: 5 residues within 4Å: Chain D: R.218 Chain E: R.218 Chain F: R.218 Ligands: CL.61, CL.77 Ligand excluded by PLIP CL.94: 5 residues within 4Å: Chain D: R.198 Chain F: V.226, A.227, G.252 Ligands: K.90 Ligand excluded by PLIP CL.95: 4 residues within 4Å: Chain C: T.177 Chain E: R.170 Chain F: G.125, G.126 Ligand excluded by PLIP

6 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 A Hydrogen bonds: A:P.78 NA.48: 2 residues within 4Å: Chain B: P.78 Chain C: N.408 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.408 NA.64: 2 residues within 4Å: Chain D: N.408 Chain F: P.78 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.408 NA.80: 2 residues within 4Å: Chain D: P.78 Chain E: N.408 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.78 NA.96: 2 residues within 4Å: Chain E: P.78 Chain F: N.408 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.408

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: 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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