SMTL ID : 3ii9.1

Crystal structure of glutaryl-coa dehydrogenase from Burkholderia pseudomallei at 1.73 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

PEG.1: 6 residues within 4Å: Chain A: F.46, V.215, R.218 Chain C: F.46, A.362, R.363 No protein-ligand interaction detected (PLIP) PEG.8: 4 residues within 4Å: Chain C: E.122, K.123, P.126, K.127 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.123, C:K.127, C:E.132 PEG.15: 7 residues within 4Å: Chain C: A.388, Q.389, T.390 Chain D: W.9, R.274, L.278 Ligands: PEG.17 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.274 PEG.17: 5 residues within 4Å: Chain D: H.8, W.9, D.10, R.274 Ligands: PEG.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.8, D:R.274 Water bridges: D:W.9

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: C.203, L.206, S.207 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:L.206, H2O.22, H2O.25, H2O.26, H2O.27 MG.11: 1 residues within 4Å: Chain C: D.10 No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PGE.3: 3 residues within 4Å: Chain A: G.36, K.37, R.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.37 Water bridges: A:E.58 PGE.7: 3 residues within 4Å: Chain C: G.36, K.37, R.41 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.37 Water bridges: C:K.37, C:R.41

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

PG4.4: 6 residues within 4Å: Chain A: Q.389 Chain B: T.6, F.7, W.9, D.10, R.274 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.274 PG4.5: 14 residues within 4Å: Chain B: R.98, S.99, S.102, V.103, L.107, F.137, L.139, T.140, L.217, L.251, A.254, I.258, V.371, Y.374 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.98, B:R.98 Water bridges: B:T.140, B:T.140, B:T.140 PG4.12: 8 residues within 4Å: Chain C: H.8, W.9, D.10, R.274 Chain D: A.388, Q.389, T.390, G.391 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.390

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain B: Q.18, L.19, A.20, R.316 No protein-ligand interaction detected (PLIP) GOL.10: 6 residues within 4Å: Chain C: S.99, V.103, L.107, A.254, I.258, Y.374 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.99 Water bridges: C:R.98 GOL.13: 3 residues within 4Å: Chain C: Q.18, A.20, R.316 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.316 GOL.14: 3 residues within 4Å: Chain D: G.36, K.37, R.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.41 GOL.16: 3 residues within 4Å: Chain D: V.152, R.154, S.165 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., User-loaded SlipChip for equipment-free multiplexed nanoliter-scale experiments. J.Am.Chem.Soc. (2010)

Release Date

2009-12-15

Peptides

Glutaryl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glutaryl-CoA dehydrogenase

Related Entries With Identical Sequence