SMTL ID : 4bgu.1

1.50 A resolution structure of the malate dehydrogenase from Haloferax volcanii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-tetramer

Ligands

23 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.1: 2 residues within 4Å: Chain A: D.27 Chain C: D.239 Ligand excluded by PLIP K.2: 4 residues within 4Å: Chain A: D.100, G.103, S.104, T.132 Ligand excluded by PLIP K.3: 2 residues within 4Å: Chain A: E.108 Ligands: 1PE.29 Ligand excluded by PLIP K.4: 1 residues within 4Å: Ligands: PGE.28 Ligand excluded by PLIP K.5: 1 residues within 4Å: Chain A: S.184 Ligand excluded by PLIP K.6: 2 residues within 4Å: Chain A: S.71, D.112 Ligand excluded by PLIP K.7: 1 residues within 4Å: Ligands: P33.30 Ligand excluded by PLIP K.31: 2 residues within 4Å: Chain B: D.27 Chain D: D.239 Ligand excluded by PLIP K.32: 4 residues within 4Å: Chain B: D.100, G.103, S.104, T.132 Ligand excluded by PLIP K.33: 2 residues within 4Å: Chain B: E.108 Ligands: 1PE.54 Ligand excluded by PLIP K.34: 1 residues within 4Å: Ligands: PGE.53 Ligand excluded by PLIP K.55: 2 residues within 4Å: Chain A: D.239 Chain C: D.27 Ligand excluded by PLIP K.56: 4 residues within 4Å: Chain C: D.100, G.103, S.104, T.132 Ligand excluded by PLIP K.57: 2 residues within 4Å: Chain C: E.108 Ligands: PG4.78 Ligand excluded by PLIP K.58: 1 residues within 4Å: Ligands: PG4.77 Ligand excluded by PLIP K.59: 1 residues within 4Å: Chain C: S.184 Ligand excluded by PLIP K.60: 2 residues within 4Å: Chain C: S.71, D.112 Ligand excluded by PLIP K.61: 2 residues within 4Å: Chain C: D.300, I.302 Ligand excluded by PLIP K.79: 2 residues within 4Å: Chain B: D.239 Chain D: D.27 Ligand excluded by PLIP K.80: 4 residues within 4Å: Chain D: D.100, G.103, S.104, T.132 Ligand excluded by PLIP K.81: 1 residues within 4Å: Chain D: E.108 Ligand excluded by PLIP K.82: 3 residues within 4Å: Chain D: G.133, D.134 Ligands: PGE.104 Ligand excluded by PLIP K.83: 1 residues within 4Å: Chain D: S.184 Ligand excluded by PLIP

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

CL.8: 1 residues within 4Å: Chain A: V.155 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: V.12 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.190 Chain D: V.243, W.278 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: I.34, P.35, K.36 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: R.88, N.120, P.121, V.122, H.175 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: R.88, K.294, Q.298 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: R.82, R.88, N.120 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain A: R.159, F.195, E.199 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: L.147, R.151, I.215, T.221 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: N.191, P.193 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: D.134, R.135 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: Y.130, D.136, R.137 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: R.135, D.136, K.139 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: N.19, R.23 Chain B: L.22 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: Q.222 Chain B: Q.222 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: K.185, D.279 Chain D: N.191, D.192 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain A: G.70, Y.109, N.110 Ligands: 1PE.29 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain A: Q.208, M.212 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain A: A.107, E.108 Ligands: 1PE.29 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain B: V.155 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain B: V.12 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain B: G.190 Chain C: W.278 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain B: I.34, P.35, K.36 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain B: N.120, P.121, V.122, H.175 Ligand excluded by PLIP CL.40: 3 residues within 4Å: Chain B: R.88, K.294, Q.298 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain B: R.82, R.88, N.120 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain B: R.159, F.195, E.199 Ligands: CL.49 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain B: R.151, I.215, T.221 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain B: N.191, P.193 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain B: A.107, G.133, D.134, R.135 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain B: Y.130, D.136, R.137 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Chain B: D.112, R.135, D.136, K.139 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain B: M.212, R.217 Ligand excluded by PLIP CL.49: 5 residues within 4Å: Chain B: F.160, P.193, A.194, F.195 Ligands: CL.42 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain B: K.2, E.28, V.30, D.67 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain B: T.61, Q.62 Ligand excluded by PLIP CL.62: 1 residues within 4Å: Chain C: V.155 Ligand excluded by PLIP CL.63: 1 residues within 4Å: Chain C: V.12 Ligand excluded by PLIP CL.64: 3 residues within 4Å: Chain B: V.243, W.278 Chain C: G.190 Ligand excluded by PLIP CL.65: 3 residues within 4Å: Chain C: I.34, P.35, K.36 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain C: R.88, N.120, P.121, V.122, H.175 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain C: R.88, K.294, Q.298 Ligand excluded by PLIP CL.68: 4 residues within 4Å: Chain C: R.82, R.88, L.91, N.120 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain C: R.159, E.199 Ligand excluded by PLIP CL.70: 4 residues within 4Å: Chain C: L.147, R.151, I.215, T.221 Ligand excluded by PLIP CL.71: 2 residues within 4Å: Chain C: N.191, P.193 Ligand excluded by PLIP CL.72: 3 residues within 4Å: Chain C: G.133, D.134, R.135 Ligand excluded by PLIP CL.73: 3 residues within 4Å: Chain C: N.19, R.23 Chain D: L.22 Ligand excluded by PLIP CL.74: 3 residues within 4Å: Chain C: M.212, R.217 Ligands: CL.76 Ligand excluded by PLIP CL.75: 4 residues within 4Å: Chain B: N.191, D.192 Chain C: K.185, D.279 Ligand excluded by PLIP CL.76: 4 residues within 4Å: Chain C: E.209, M.212, R.217 Ligands: CL.74 Ligand excluded by PLIP CL.84: 1 residues within 4Å: Chain D: V.155 Ligand excluded by PLIP CL.85: 1 residues within 4Å: Chain D: V.12 Ligand excluded by PLIP CL.86: 2 residues within 4Å: Chain A: W.278 Chain D: G.190 Ligand excluded by PLIP CL.87: 3 residues within 4Å: Chain D: I.34, P.35, K.36 Ligand excluded by PLIP CL.88: 4 residues within 4Å: Chain D: N.120, P.121, V.122, H.175 Ligand excluded by PLIP CL.89: 3 residues within 4Å: Chain D: R.88, K.294, Q.298 Ligand excluded by PLIP CL.90: 3 residues within 4Å: Chain D: R.82, R.88, N.120 Ligand excluded by PLIP CL.91: 3 residues within 4Å: Chain D: R.159, F.195, E.199 Ligand excluded by PLIP CL.92: 4 residues within 4Å: Chain D: L.147, R.151, I.215, T.221 Ligand excluded by PLIP CL.93: 3 residues within 4Å: Chain D: F.160, N.191, P.193 Ligand excluded by PLIP CL.94: 2 residues within 4Å: Chain D: G.133, D.134 Ligand excluded by PLIP CL.95: 3 residues within 4Å: Chain D: Y.130, D.136, R.137 Ligand excluded by PLIP CL.96: 4 residues within 4Å: Chain D: D.112, R.135, D.136, K.139 Ligand excluded by PLIP CL.97: 3 residues within 4Å: Chain C: L.22 Chain D: N.19, R.23 Ligand excluded by PLIP CL.98: 2 residues within 4Å: Chain D: M.212, R.217 Ligand excluded by PLIP CL.99: 2 residues within 4Å: Chain C: Q.222 Chain D: Q.222 Ligand excluded by PLIP CL.100: 1 residues within 4Å: Chain D: G.70 Ligand excluded by PLIP CL.101: 1 residues within 4Å: Chain D: L.204 Ligand excluded by PLIP CL.102: 2 residues within 4Å: Chain D: E.257, R.296 Ligand excluded by PLIP CL.103: 5 residues within 4Å: Chain C: Y.54 Chain D: R.153, A.169, T.170, P.245 Ligand excluded by PLIP

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.27: 1 residues within 4Å: Chain D: D.168 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain D Hydrogen bonds: A:R.153, D:D.168 Water bridges: A:R.153, A:K.165, A:K.165, A:K.165, A:V.167, D:R.153, D:R.153, D:R.153, D:K.165, D:K.165 TRS.52: 2 residues within 4Å: Chain B: K.165, D.168 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.153, B:K.165 Water bridges: B:R.153, B:R.153, B:R.153, C:K.165, C:D.168, C:D.168

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.28: 6 residues within 4Å: Chain A: Y.130, E.131, G.133, D.134, R.135 Ligands: K.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.131, A:E.131, A:D.134 PGE.53: 6 residues within 4Å: Chain B: Y.130, E.131, G.133, D.134, R.135 Ligands: K.34 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.131, B:E.131, B:E.131 PGE.104: 6 residues within 4Å: Chain D: Y.130, E.131, G.133, D.134, R.135 Ligands: K.82 4 PLIP interactions: 4 interactions with chain D Water bridges: D:Y.130, D:E.131, D:E.131, D:E.131

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.29: 9 residues within 4Å: Chain A: A.69, A.107, E.108, Y.109, N.110, D.111 Ligands: K.3, CL.24, CL.26 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.108, A:E.108 Water bridges: A:Y.109 1PE.54: 6 residues within 4Å: Chain B: A.107, E.108, Y.109, N.110, D.111 Ligands: K.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.108

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.30: 5 residues within 4Å: Chain A: F.254, G.255, Y.256, D.289 Ligands: K.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.286

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.77: 6 residues within 4Å: Chain C: Y.130, E.131, G.133, D.134, R.135 Ligands: K.58 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.131, C:E.131 PG4.78: 6 residues within 4Å: Chain C: A.107, E.108, Y.109, N.110, D.111 Ligands: K.57 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Talon, R. et al., Insight Into Structural Evolution of Extremophilic Proteins. To be Published

Release Date

2014-04-16

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

MALATE DEHYDROGENASE