SMTL ID : 2x0r.1

R207S, R292S Mutant of Malate Dehydrogenase from the Halophilic Archeon Haloarcula marismortui (HoloForm)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.92 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: G.8, A.10, G.11, T.12, V.13, G.14, D.34, I.35, K.38, Y.66, T.78, A.79, G.80, I.99, I.103, T.119, S.120, N.121, V.123, F.144, G.145, L.148, H.176, T.222, P.226 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.13, A:L.148, A:P.226 Hydrogen bonds: A:T.12, A:T.12, A:V.13, A:G.14, A:G.80, A:T.119, A:T.119, A:N.121 NAD.5: 23 residues within 4Å: Chain B: V.7, G.8, A.10, G.11, T.12, V.13, D.34, I.35, Y.66, T.78, A.79, G.80, R.83, I.99, T.119, S.120, N.121, V.123, F.144, G.145, L.148, H.176, T.222 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.222 Hydrogen bonds: B:T.12, B:T.12, B:V.13, B:Y.66, B:A.79, B:G.80, B:R.83, B:R.83, B:D.102, B:N.121, B:F.144 Water bridges: B:A.10, B:G.14 NAD.12: 25 residues within 4Å: Chain C: G.8, A.10, G.11, T.12, V.13, G.14, D.34, I.35, K.38, Y.66, T.78, A.79, G.80, I.99, I.103, T.119, S.120, N.121, V.123, F.144, G.145, L.148, H.176, T.222, P.226 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.13, C:L.148, C:P.226 Hydrogen bonds: C:T.12, C:T.12, C:T.12, C:V.13, C:G.14, C:Y.66, C:G.80, C:T.119, C:N.121 NAD.16: 23 residues within 4Å: Chain D: V.7, G.8, A.10, G.11, T.12, V.13, D.34, I.35, Y.66, T.78, A.79, G.80, R.83, I.99, T.119, S.120, N.121, V.123, F.144, G.145, L.148, H.176, T.222 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:T.222 Hydrogen bonds: D:T.12, D:V.13, D:A.79, D:G.80, D:R.83, D:R.83, D:D.102, D:T.119, D:N.121, D:F.144 Water bridges: D:A.10, D:G.14, D:T.78

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

CL.2: 5 residues within 4Å: Chain A: K.186, W.279, D.280 Chain D: T.192, D.193 Ligand excluded by PLIP CL.3: 5 residues within 4Å: Chain A: R.24, R.228, A.231, H.232, E.235 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: K.186, D.280 Chain C: T.192, D.193 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: R.24, R.228, A.231, H.232, E.235 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: T.192, D.193 Chain C: K.186, W.279, D.280 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: R.24, R.228, A.231, H.232, E.235 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: T.192, D.193 Chain D: K.186, D.280 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: R.24, R.228, A.231, H.232, E.235 Ligand excluded by PLIP

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

NA.4: 3 residues within 4Å: Chain A: D.25, A.27, D.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.27, A:D.28 NA.8: 3 residues within 4Å: Chain B: K.186, S.188 Chain C: S.188 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.186, B:S.188, C:S.188 Water bridges: C:E.169 NA.9: 6 residues within 4Å: Chain B: I.21, A.22, D.25, I.26, A.27, T.59 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.25, B:I.26, B:A.27, B:A.27 NA.10: 1 residues within 4Å: Chain B: Q.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.63 NA.11: 6 residues within 4Å: Chain B: D.124, N.127, R.128, S.248, V.249, A.261 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.124, B:R.128 NA.15: 3 residues within 4Å: Chain C: D.25, A.27, D.28 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.27 NA.19: 3 residues within 4Å: Chain A: S.188 Chain D: K.186, S.188 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.188, D:S.188, D:D.193 NA.20: 6 residues within 4Å: Chain D: I.21, A.22, D.25, I.26, A.27, T.59 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.21, D:D.25, D:I.26, D:A.27, D:T.59 NA.21: 1 residues within 4Å: Chain D: Q.63 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.63, D:Q.63 NA.22: 6 residues within 4Å: Chain D: D.124, N.127, R.128, S.248, V.249, A.261 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.128, D:S.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Irimia, A. et al., The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase are Modulated by Solvent Components as Shown by Crystallographic and Biochemical Studies. J.Mol.Biol. (2003)

Release Date

2009-12-29

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

MALATE DEHYDROGENASE