SMTL ID : 8p5r.1

Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.56 Å

Oligo State

hetero-10-6-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: R.563, N.701, I.703, G.704, F.705, R.766, H.770 Ligands: TPP.3 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain B: D.668, A.669, N.701, I.703 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.668, B:I.703 MG.9: 5 residues within 4Å: Chain C: G.667, D.668, N.701, I.703 Ligands: TPP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.668 MG.12: 6 residues within 4Å: Chain D: G.667, D.668, A.669, N.701, I.703 Ligands: TPP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.668 MG.15: 6 residues within 4Å: Chain E: D.668, A.669, N.701, I.703, G.704 Ligands: TPP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.668, E:I.703 MG.18: 3 residues within 4Å: Chain F: G.667, D.668 Ligands: TPP.20 No protein-ligand interaction detected (PLIP)

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: E.311 Chain C: E.311 Chain E: E.311 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.311, A:E.311 CA.6: 5 residues within 4Å: Chain B: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain B: E.311 Chain D: E.311 Chain F: E.311 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain F, 1 interactions with chain D Metal complexes: B:E.311, F:E.311, D:E.311 CA.10: 5 residues within 4Å: Chain C: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain D: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP) CA.16: 5 residues within 4Å: Chain E: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP) CA.19: 5 residues within 4Å: Chain F: D.1027, H.1078, G.1079, D.1081, G.1082 No protein-ligand interaction detected (PLIP)

6 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 21 residues within 4Å: Chain A: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, V.699, N.701, I.703, G.704, F.705, H.770 Chain B: Q.924, L.973, E.975, Q.999, F.1003 Ligands: MG.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.627, A:L.629, A:D.668, A:A.669, A:A.670, A:N.701, A:I.703 Salt bridges: A:R.563 pi-Stacking: A:H.770, B:F.1003 Hydrophobic interactions: B:L.973 TPP.7: 20 residues within 4Å: Chain A: Q.924, L.973, E.975, Q.999, F.1003 Chain B: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, N.701, I.703, G.704, F.705, H.770 Ligands: MG.5 12 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.1003 pi-Stacking: A:F.1003 Hydrogen bonds: B:S.627, B:L.629, B:D.668, B:A.669, B:A.670, B:N.701, B:I.703, B:F.705 Salt bridges: B:R.563, B:H.770 TPP.11: 20 residues within 4Å: Chain C: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, Q.674, N.701, I.703, G.704, H.770 Chain D: Q.924, L.973, E.975, Q.999, F.1003 Ligands: MG.9 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.627, C:L.629, C:D.668, C:A.669, C:A.670, C:N.701, C:N.701 Salt bridges: C:R.563, C:H.770 Hydrophobic interactions: D:L.973, D:L.973 pi-Stacking: D:F.1003 TPP.14: 21 residues within 4Å: Chain C: Q.924, L.973, E.975, Q.999, F.1003 Chain D: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, Q.674, N.701, I.703, G.704, F.705, H.770 Ligands: MG.12 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.627, D:L.629, D:D.668, D:A.669, D:A.670, D:N.701, D:I.703 Salt bridges: D:R.563, D:H.770 Hydrophobic interactions: C:L.973 pi-Stacking: C:F.1003 TPP.17: 19 residues within 4Å: Chain E: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, N.701, I.703, G.704, H.770 Chain F: Q.924, L.973, E.975, Q.999, F.1003 Ligands: MG.15 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain E Hydrophobic interactions: F:L.973 pi-Stacking: F:F.1003 Hydrogen bonds: E:S.627, E:L.629, E:D.668, E:A.669, E:A.670, E:N.701 Salt bridges: E:R.563, E:H.770 TPP.20: 21 residues within 4Å: Chain E: Q.924, L.973, E.975, Q.999, F.1003 Chain F: R.563, H.594, S.627, H.628, L.629, G.667, D.668, A.669, A.670, N.701, I.703, G.704, F.705, R.766, H.770 Ligands: MG.18 12 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.705, E:L.973 Hydrogen bonds: F:S.627, F:L.629, F:D.668, F:A.669, F:A.670, F:N.701, F:R.766 Salt bridges: F:R.563, F:H.770 pi-Stacking: E:F.1003

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L. et al., High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Multifunctional 2-oxoglutarate metabolism enzyme: ABCDEFMNOP
Glycogen accumulation regulator GarA: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

M
N

N
O

O
P

P
Q

G
G

H
H

I
I

J
J

K
K

L
L

Multifunctional 2-oxoglutarate metabolism enzyme

Glycogen accumulation regulator GarA