SMTL ID : 6qss.1

Crystal Structure of Ignicoccus islandicus malate dehydrogenase co-crystallized with 10 mM Tb-Xo4

Coordinates

PDB Format

Method

SOLUTION SCATTERING 1.89 Å

Oligo State

homo-tetramer

Ligands

2 x 7MT: Tb-Xo4(Non-covalent)

7MT.1: 4 residues within 4Å: Chain A: S.91, R.93, D.94 Ligands: TB.5 7 PLIP interactions: 7 interactions with chain A, Hydrogen bonds: A:S.91 Salt bridges: A:R.93, A:R.93, A:D.94, A:D.94, A:D.94 Metal complexes: A:D.94 7MT.18: 4 residues within 4Å: Chain D: S.91, R.93, D.94 Ligands: TB.23 9 PLIP interactions: 9 interactions with chain D, Hydrogen bonds: D:S.91 Salt bridges: D:R.93, D:R.93, D:D.94, D:D.94, D:D.94 pi-Cation interactions: D:R.93 Metal complexes: D:D.94, D:D.94

18 x TB: TERBIUM(III) ION(Non-covalent)(Non-functional Binders)

TB.2: 1 residues within 4Å: Chain A: D.135 Ligand excluded by PLIP TB.3: 3 residues within 4Å: Chain A: R.92, E.180, E.181 Ligand excluded by PLIP TB.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.5: 2 residues within 4Å: Chain A: D.94 Ligands: 7MT.1 Ligand excluded by PLIP TB.8: 1 residues within 4Å: Ligands: TB.11 Ligand excluded by PLIP TB.9: 1 residues within 4Å: Chain B: E.181 Ligand excluded by PLIP TB.10: 1 residues within 4Å: Chain B: E.288 Ligand excluded by PLIP TB.11: 2 residues within 4Å: Chain B: E.180 Ligands: TB.8 Ligand excluded by PLIP TB.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP TB.14: 1 residues within 4Å: Chain C: D.94 Ligand excluded by PLIP TB.15: 1 residues within 4Å: Chain C: E.292 Ligand excluded by PLIP TB.16: 1 residues within 4Å: Chain C: E.180 Ligand excluded by PLIP TB.17: 1 residues within 4Å: Chain C: E.181 Ligand excluded by PLIP TB.19: 1 residues within 4Å: Chain D: E.73 Ligand excluded by PLIP TB.20: 1 residues within 4Å: Chain D: E.288 Ligand excluded by PLIP TB.21: 1 residues within 4Å: Chain D: E.181 Ligand excluded by PLIP TB.22: 1 residues within 4Å: Chain D: E.180 Ligand excluded by PLIP TB.23: 2 residues within 4Å: Chain D: D.94 Ligands: 7MT.18 Ligand excluded by PLIP

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

CL.6: 1 residues within 4Å: Chain A: E.67 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: N.124, P.125 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: G.41, A.43, K.44, E.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roche, J. et al., The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization. J.Struct.Biol. (2019)

Release Date

2019-07-17

Peptides

Malate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Malate dehydrogenase