SMTL ID : 3swo.1

Crystal structure of a glutaryl-coa dehydrogenase from mycobacterium smegmatis in complex with FADH2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-tetramer

Ligands

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.1: 30 residues within 4Å: Chain A: F.143, L.145, T.146, G.151, S.152, W.176, I.177, T.178, L.219, T.224, S.372, T.375, Y.376, E.377, T.379, E.381, M.382, F.397 Chain C: Q.293 Chain D: R.282, V.284, F.285, L.289, Y.292, T.350, L.351, G.353, G.354, I.357 Ligands: EDO.3 35 PLIP interactions: 9 interactions with chain D, 25 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:T.350, D:G.354, A:F.143, A:L.145, A:T.146, A:T.146, A:T.146, A:S.152, A:S.152, A:T.178, A:T.178, A:E.377, A:T.379, A:E.381, A:F.397, C:Q.293 Water bridges: D:Y.278, D:R.282, D:R.282, D:T.295, D:S.355, A:F.143, A:T.146, A:G.151, A:N.153, A:G.378, A:G.378, A:G.378 Salt bridges: D:R.282, D:R.282 Hydrophobic interactions: A:W.176, A:L.219, A:T.224, A:Y.376 pi-Stacking: A:Y.376 FDA.5: 30 residues within 4Å: Chain B: F.143, L.145, T.146, G.151, S.152, W.176, I.177, T.178, L.219, T.224, S.372, T.375, Y.376, E.377, T.379, E.381, M.382, F.397 Chain C: R.282, V.284, F.285, L.289, Y.292, T.350, L.351, G.353, G.354, I.357 Chain D: Q.293 Ligands: EDO.7 32 PLIP interactions: 24 interactions with chain B, 7 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: B:W.176, B:L.219, B:T.224, B:Y.376 Hydrogen bonds: B:F.143, B:L.145, B:T.146, B:T.146, B:T.146, B:S.152, B:S.152, B:T.178, B:T.178, B:T.178, B:E.377, B:T.379, B:T.379, B:F.397, C:T.350, C:G.354, D:Q.293 Water bridges: B:F.143, B:T.146, B:G.151, B:N.153, B:G.378, C:R.282, C:R.282, C:S.355 pi-Stacking: B:Y.376 Salt bridges: C:R.282, C:R.282 FDA.16: 29 residues within 4Å: Chain A: Q.293 Chain B: R.282, V.284, F.285, L.289, Y.292, T.350, L.351, G.353, G.354, I.357 Chain C: F.143, L.145, T.146, G.151, S.152, W.176, I.177, T.178, L.219, S.372, T.375, Y.376, E.377, T.379, E.381, M.382, F.397 Ligands: EDO.17 31 PLIP interactions: 23 interactions with chain C, 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:W.176, C:L.219, C:Y.376 Hydrogen bonds: C:F.143, C:L.145, C:T.146, C:T.146, C:T.146, C:S.152, C:S.152, C:T.178, C:T.178, C:T.178, C:E.377, C:T.379, C:T.379, C:F.397, B:T.350, B:G.354, A:Q.293 Water bridges: C:F.143, C:T.146, C:G.151, C:N.153, C:G.378, B:R.282, B:R.282, B:S.355 pi-Stacking: C:Y.376 Salt bridges: B:R.282, B:R.282 FDA.27: 29 residues within 4Å: Chain A: R.282, V.284, F.285, L.289, Y.292, T.350, L.351, G.353, G.354, I.357 Chain B: Q.293 Chain D: F.143, L.145, T.146, G.151, S.152, W.176, I.177, T.178, L.219, S.372, T.375, Y.376, E.377, T.379, E.381, M.382, F.397 Ligands: EDO.28 31 PLIP interactions: 8 interactions with chain A, 22 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:T.350, A:G.354, D:F.143, D:L.145, D:T.146, D:T.146, D:T.146, D:S.152, D:S.152, D:T.178, D:T.178, D:E.377, D:T.379, D:E.381, D:F.397, B:Q.293 Water bridges: A:Y.278, A:R.282, A:R.282, A:S.355, D:F.143, D:T.146, D:G.151, D:N.153, D:G.378 Salt bridges: A:R.282, A:R.282 Hydrophobic interactions: D:W.176, D:L.219, D:Y.376 pi-Stacking: D:Y.376

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: R.346, A.367, E.371 Chain D: R.346, A.367, E.371 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:R.346, D:A.367, D:E.371, A:R.346, A:A.367, A:E.371 EDO.3: 8 residues within 4Å: Chain A: R.104, S.105, S.108, V.109, L.113, Y.376, E.377 Ligands: FDA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.104, A:S.105, A:S.108, A:E.377, A:E.377 Water bridges: A:E.377 EDO.4: 6 residues within 4Å: Chain A: G.151, L.250, L.253, R.257, E.377, G.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.257 Water bridges: A:R.257, A:E.377 EDO.6: 6 residues within 4Å: Chain B: R.346, A.367, E.371 Chain C: R.346, A.367, E.371 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.346, B:A.367, B:E.371, C:R.346, C:A.367 EDO.7: 8 residues within 4Å: Chain B: R.104, S.105, S.108, V.109, T.178, Y.376, E.377 Ligands: FDA.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.104, B:S.105, B:S.108 Water bridges: B:E.377 EDO.8: 6 residues within 4Å: Chain B: P.154, L.250, L.253, R.257, E.377, G.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.257 Water bridges: B:R.257 EDO.17: 8 residues within 4Å: Chain C: R.104, S.105, S.108, V.109, T.178, Y.376, E.377 Ligands: FDA.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.104, C:S.105, C:S.108 Water bridges: C:E.377, C:E.377 EDO.18: 7 residues within 4Å: Chain C: G.151, P.154, L.250, L.253, R.257, E.377, G.378 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.257 Water bridges: C:R.257 EDO.28: 8 residues within 4Å: Chain D: R.104, S.105, S.108, V.109, L.113, Y.376, E.377 Ligands: FDA.27 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.104, D:S.105, D:S.108, D:E.377, D:E.377 Water bridges: D:E.377 EDO.29: 8 residues within 4Å: Chain D: G.151, S.152, P.154, L.250, L.253, R.257, E.377, G.378 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.257 Water bridges: D:T.379

15 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.9: 4 residues within 4Å: Chain C: T.36, L.69 Ligands: UNX.10, UNX.11 No protein-ligand interaction detected (PLIP) UNX.10: 6 residues within 4Å: Chain C: L.69, G.70, V.71, M.74 Ligands: UNX.9, UNX.11 No protein-ligand interaction detected (PLIP) UNX.11: 4 residues within 4Å: Chain C: L.69 Ligands: UNX.9, UNX.10, UNX.12 No protein-ligand interaction detected (PLIP) UNX.12: 3 residues within 4Å: Ligands: UNX.11, UNX.13, UNX.14 No protein-ligand interaction detected (PLIP) UNX.13: 4 residues within 4Å: Chain C: N.68, L.69 Ligands: UNX.12, UNX.14 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain C: T.36 Ligands: UNX.12, UNX.13, UNX.15 No protein-ligand interaction detected (PLIP) UNX.15: 3 residues within 4Å: Chain C: T.36, L.69 Ligands: UNX.14 No protein-ligand interaction detected (PLIP) UNX.19: 6 residues within 4Å: Chain D: L.69, G.70, V.71, M.74 Ligands: UNX.20, UNX.21 No protein-ligand interaction detected (PLIP) UNX.20: 4 residues within 4Å: Chain D: T.36, L.69 Ligands: UNX.19, UNX.21 No protein-ligand interaction detected (PLIP) UNX.21: 6 residues within 4Å: Chain D: L.69 Ligands: UNX.19, UNX.20, UNX.22, UNX.23, UNX.24 No protein-ligand interaction detected (PLIP) UNX.22: 2 residues within 4Å: Ligands: UNX.21, UNX.23 No protein-ligand interaction detected (PLIP) UNX.23: 3 residues within 4Å: Ligands: UNX.21, UNX.22, UNX.24 No protein-ligand interaction detected (PLIP) UNX.24: 3 residues within 4Å: Ligands: UNX.21, UNX.23, UNX.25 No protein-ligand interaction detected (PLIP) UNX.25: 3 residues within 4Å: Chain D: L.69 Ligands: UNX.24, UNX.26 No protein-ligand interaction detected (PLIP) UNX.26: 2 residues within 4Å: Chain D: L.69 Ligands: UNX.25 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2011-08-03

Peptides

Glutaryl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glutaryl-CoA dehydrogenase