SMTL ID : 4bgv.1

1.8 A resolution structure of the malate dehydrogenase from Picrophilus torridus in its apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-tetramer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: A.12, Y.225, G.228, S.229, F.231 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.42 Hydrogen bonds: A:S.229 PEG.2: 2 residues within 4Å: Chain A: I.23 Chain B: I.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.23 PEG.4: 7 residues within 4Å: Chain B: A.12, Y.225, T.227, G.228, S.229, F.231 Ligands: PEG.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:K.42, A:K.42 Hydrogen bonds: B:S.229 PEG.5: 3 residues within 4Å: Chain A: F.231 Chain B: F.231 Ligands: PEG.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:G.11, A:K.42, B:K.42, B:K.42 PEG.6: 4 residues within 4Å: Chain B: E.164, L.201, L.202, P.203 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.164 PEG.7: 4 residues within 4Å: Chain A: E.199, D.200, L.201, L.202 No protein-ligand interaction detected (PLIP) PEG.9: 5 residues within 4Å: Chain C: A.12, Y.225, G.228, S.229, F.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.229 PEG.10: 2 residues within 4Å: Chain C: I.23 Chain D: I.23 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.24 PEG.11: 5 residues within 4Å: Chain C: A.12, K.42, F.231 Chain D: F.231 Ligands: PEG.12 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:K.42, D:G.11, D:K.42 PEG.12: 5 residues within 4Å: Chain D: Y.225, G.228, S.229, F.231 Ligands: PEG.11 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Water bridges: C:K.42, C:K.42 Hydrogen bonds: D:S.229 PEG.13: 4 residues within 4Å: Chain D: E.199, D.200, L.201, L.202 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.201 Water bridges: D:R.204

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 4 residues within 4Å: Chain B: E.40, G.61, F.62, K.69 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.40 Water bridges: B:E.40, B:E.40, B:C.63, B:C.63, B:K.69, B:K.69 Salt bridges: B:K.69, B:K.69

1 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.8: 5 residues within 4Å: Chain B: P.197, D.200 Chain C: R.189, Y.190, K.292 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.189, C:R.189, C:Y.190

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