SMTL ID : 6ihe.1

Crystal structure of Malate dehydrogenase from Metallosphaera sedula

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 residues within 4Å: Chain A: G.9, K.10, I.11, Y.31, D.32, I.33, I.34, L.37, S.76, A.77, G.78, K.79, P.80, N.94, I.97, V.117, A.118, N.119, V.143, T.217, P.221 Ligands: MLT.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.11, A:P.221 Hydrogen bonds: A:K.10, A:I.11, A:Y.31, A:I.33, A:G.78, A:K.79, A:R.81, A:N.94, A:N.119, A:N.119 Water bridges: A:G.9, A:G.12 Salt bridges: A:K.10, A:K.10 NAD.10: 24 residues within 4Å: Chain B: G.7, A.8, G.9, K.10, I.11, Y.31, D.32, I.33, I.34, L.37, S.76, A.77, G.78, K.79, P.80, N.94, I.97, V.117, A.118, N.119, V.143, T.217, P.221 Ligands: MLT.11 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.11, B:P.221 Hydrogen bonds: B:K.10, B:I.11, B:G.12, B:I.33, B:G.78, B:G.78, B:N.94, B:N.119, B:N.119 Water bridges: B:G.9, B:R.81, B:D.100, B:G.140 Salt bridges: B:K.10, B:K.10 NAD.20: 22 residues within 4Å: Chain C: G.9, K.10, I.11, Y.31, D.32, I.33, I.34, L.37, S.76, A.77, G.78, K.79, P.80, N.94, I.97, V.117, A.118, N.119, V.143, T.217, P.221 Ligands: MLT.21 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.11, C:P.221 Hydrogen bonds: C:K.10, C:I.11, C:I.33, C:G.78, C:K.79, C:R.81, C:N.94, C:N.119, C:N.119 Water bridges: C:G.9, C:G.12 Salt bridges: C:K.10, C:K.10 NAD.29: 24 residues within 4Å: Chain D: G.7, A.8, G.9, K.10, I.11, Y.31, D.32, I.33, I.34, L.37, S.76, A.77, G.78, K.79, P.80, N.94, I.97, V.117, A.118, N.119, V.143, T.217, P.221 Ligands: MLT.30 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.11, D:P.221 Hydrogen bonds: D:K.10, D:I.11, D:G.12, D:I.33, D:G.78, D:G.78, D:N.94, D:N.119, D:N.119 Water bridges: D:G.9, D:R.81, D:G.140 Salt bridges: D:K.10, D:K.10

4 x MLT: D-MALATE(Non-covalent)

MLT.2: 9 residues within 4Å: Chain A: R.81, R.87, N.119, R.147, H.171, P.207, I.211, T.217 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.87, A:N.119, A:H.171, A:T.217, A:T.217 Salt bridges: A:R.81, A:R.87, A:R.87, A:R.147 MLT.11: 9 residues within 4Å: Chain B: R.81, R.87, N.119, R.147, H.171, P.207, I.211, T.217 Ligands: NAD.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.87, B:N.119, B:H.171, B:T.217, B:T.217 Water bridges: B:T.217 Salt bridges: B:R.81, B:R.87, B:R.87, B:R.147 MLT.21: 9 residues within 4Å: Chain C: R.81, R.87, N.119, R.147, H.171, P.207, I.211, T.217 Ligands: NAD.20 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.87, C:N.119, C:H.171, C:T.217 Salt bridges: C:R.81, C:R.87, C:R.87, C:R.147 MLT.30: 9 residues within 4Å: Chain D: R.81, R.87, N.119, R.147, H.171, P.207, I.211, T.217 Ligands: NAD.29 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.87, D:N.119, D:H.171, D:T.217 Water bridges: D:T.217 Salt bridges: D:R.81, D:R.87, D:R.87, D:R.147

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.130, Y.131, K.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.131, A:Y.131, A:K.133 Water bridges: A:K.130 GOL.12: 5 residues within 4Å: Chain A: K.230, E.236 Chain B: K.230, E.236, R.238 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.230, A:K.230, A:E.236 Water bridges: B:E.236, B:R.238, A:E.236 GOL.22: 3 residues within 4Å: Chain C: K.130, Y.131, K.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.131, C:K.133 Water bridges: C:K.130 GOL.31: 5 residues within 4Å: Chain C: K.230, E.236 Chain D: K.230, E.236, R.238 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.230, C:K.230, C:E.236 Water bridges: D:R.238

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

PGE.4: 4 residues within 4Å: Chain A: D.26, E.27, K.55, N.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.26 Water bridges: A:A.56, A:A.56 PGE.5: 8 residues within 4Å: Chain A: F.166, S.180, T.181, P.258, L.272 Chain B: S.264, G.266, P.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.272 PGE.13: 1 residues within 4Å: Chain B: K.250 No protein-ligand interaction detected (PLIP) PGE.14: 9 residues within 4Å: Chain A: K.185, G.186 Chain B: G.111, I.113, F.135, S.263, S.264, I.265 Ligands: PG4.8 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.185, B:I.265 PGE.15: 3 residues within 4Å: Chain B: S.68, S.107, K.108 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.108 PGE.23: 4 residues within 4Å: Chain C: D.26, E.27, K.55, N.57 2 PLIP interactions: 2 interactions with chain C Water bridges: C:A.56, C:A.56 PGE.24: 8 residues within 4Å: Chain C: F.166, S.180, T.181, P.258, L.272 Chain D: S.264, G.266, P.267 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.272 PGE.32: 1 residues within 4Å: Chain D: K.250 No protein-ligand interaction detected (PLIP) PGE.33: 9 residues within 4Å: Chain C: K.185, G.186 Chain D: G.111, I.113, F.135, S.263, S.264, I.265 Ligands: PG4.27 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.185, D:I.265 PGE.34: 3 residues within 4Å: Chain D: S.68, S.107, K.108 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.108

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: S.18, S.22 Chain C: Y.17, V.21, K.52 Ligands: EDO.25 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.52, A:S.18 EDO.16: 4 residues within 4Å: Chain B: W.279, N.282, S.283, K.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.279 EDO.17: 4 residues within 4Å: Chain A: P.267 Chain B: F.166, T.181, L.273 No protein-ligand interaction detected (PLIP) EDO.18: 5 residues within 4Å: Chain B: S.18, V.21, S.22 Chain D: V.21, K.52 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:K.52, B:S.22 EDO.25: 6 residues within 4Å: Chain A: Y.17, V.21, K.52 Chain C: S.18, S.22 Ligands: EDO.6 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:S.18, A:Y.17, A:K.52 EDO.35: 4 residues within 4Å: Chain D: W.279, N.282, S.283, K.286 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:W.279 EDO.36: 4 residues within 4Å: Chain C: P.267 Chain D: F.166, T.181, L.273 No protein-ligand interaction detected (PLIP) EDO.37: 5 residues within 4Å: Chain B: V.21, K.52 Chain D: S.18, V.21, S.22 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.52, D:S.22

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

PG4.7: 7 residues within 4Å: Chain A: A.1, D.71, G.111, I.113 Chain B: T.161, S.162, K.185 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.71, A:D.71, B:K.185 PG4.8: 9 residues within 4Å: Chain A: T.161, S.162, K.185 Chain B: D.71, G.111, A.112, I.113, S.263 Ligands: PGE.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.185 PG4.26: 7 residues within 4Å: Chain C: A.1, D.71, G.111, I.113 Chain D: T.161, S.162, K.185 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:K.185, C:D.71, C:D.71, C:D.71 Water bridges: C:A.1, C:A.1 PG4.27: 9 residues within 4Å: Chain C: T.161, S.162, K.185 Chain D: D.71, G.111, A.112, I.113, S.263 Ligands: PGE.33 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.185

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 2 residues within 4Å: Chain A: E.275, K.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.275, A:E.275 PEG.19: 3 residues within 4Å: Chain B: E.198, D.201, Y.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.201 PEG.28: 2 residues within 4Å: Chain C: E.275, K.276 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.275 PEG.38: 3 residues within 4Å: Chain D: E.198, D.201, Y.202 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, D. et al., Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula. Biochem. Biophys. Res. Commun. (2019)

Release Date

2019-02-06

Peptides

Malate dehydrogenase (NAD): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Malate dehydrogenase (NAD)