SMTL ID : 6vef.1

Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 12 residues within 4Å: Chain A: S.218, H.229, R.253, R.256, M.437, S.441, F.442, W.444, L.448, T.584, R.621, M.622 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.218, A:R.256, A:T.584, A:T.584, A:M.622 Salt bridges: A:H.229, A:R.253 pi-Stacking: A:W.444, A:W.444 AMP.4: 12 residues within 4Å: Chain B: S.218, H.229, R.253, R.256, M.437, S.441, F.442, W.444, L.448, T.584, R.621, M.622 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.218, B:R.256, B:T.584, B:T.584, B:M.622 Salt bridges: B:H.229, B:R.253 pi-Stacking: B:W.444, B:W.444

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 11 residues within 4Å: Chain A: E.527, D.528, L.570, Q.596, F.600 Chain B: H.176, R.177, L.239, D.273, G.309, F.310 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:E.527, A:D.528, A:Q.596, B:G.309 Hydrophobic interactions: B:L.239 Salt bridges: B:H.176, B:H.176, B:R.177 OAA.3: 11 residues within 4Å: Chain A: H.176, R.177, L.239, D.273, G.309, F.310 Chain B: E.527, D.528, L.570, Q.596, F.600 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:E.527, B:D.528, B:Q.596, A:G.309 Hydrophobic interactions: A:L.239 Salt bridges: A:H.176, A:H.176, A:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, H., Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA. To Be Published

Release Date

2021-01-06

Peptides

2-oxoglutarate dehydrogenase E1 component: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxoglutarate dehydrogenase E1 component