SMTL ID : 4ubv.1

Structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis with an partially acetylated cysteine in complex with acetyl-CoA and CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

1 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.1: 18 residues within 4Å: Chain A: C.101, Q.159, F.160, R.229, T.231, L.236, L.239, A.250, G.251, S.253, S.254, I.256, L.296, A.325, H.355, V.357, C.385 Ligands: COA.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.160, A:F.160, A:L.296 Hydrogen bonds: A:Q.159, A:R.229, A:T.231, A:S.254, A:S.254, A:S.254, A:N.323 Water bridges: A:R.25, A:R.25, A:I.256 pi-Cation interactions: A:R.229

2 x COA: COENZYME A(Non-covalent)

COA.2: 10 residues within 4Å: Chain A: L.136, Q.159, F.160, Q.185, R.229, T.231, L.239, A.250, I.256 Ligands: ACO.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.160 Hydrogen bonds: A:Q.185, A:R.229, A:T.231 Water bridges: A:R.25 pi-Cation interactions: A:R.229, A:R.229 COA.11: 17 residues within 4Å: Chain B: C.101, Q.159, F.160, Q.185, R.229, E.230, T.231, L.239, A.250, G.251, S.253, S.254, Q.255, I.256, A.325, F.326, H.355 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.326 Hydrogen bonds: B:K.24, B:Q.185, B:R.229, B:R.229, B:T.231, B:S.254, B:S.254, B:S.254, B:I.256 Water bridges: B:S.254 Salt bridges: B:R.229 pi-Cation interactions: B:R.229, B:R.229

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 1 residues within 4Å: Ligands: DIO.6 No protein-ligand interaction detected (PLIP) SO4.4: 5 residues within 4Å: Chain A: L.32, E.36, A.40, I.204, Q.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.205 SO4.12: 3 residues within 4Å: Chain B: V.283, K.309, A.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.281

7 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.5: 3 residues within 4Å: Chain A: R.25, N.26, G.27 No protein-ligand interaction detected (PLIP) DIO.6: 3 residues within 4Å: Chain A: R.272, L.276 Ligands: SO4.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.272 DIO.13: 4 residues within 4Å: Chain B: H.56, A.57, G.58, P.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.58 Water bridges: B:A.57 DIO.14: 5 residues within 4Å: Chain B: W.28, L.221, V.222, F.223, R.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.223, B:R.224 DIO.15: 2 residues within 4Å: Chain B: L.182, M.233 No protein-ligand interaction detected (PLIP) DIO.16: 1 residues within 4Å: Chain B: D.198 No protein-ligand interaction detected (PLIP) DIO.17: 3 residues within 4Å: Chain B: W.28, R.220 Ligands: GOL.24 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: W.28, R.220 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: P.89, E.90, H.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.90, A:H.91, A:H.91 GOL.9: 4 residues within 4Å: Chain A: K.168, R.169, R.170, G.171 No protein-ligand interaction detected (PLIP) GOL.10: 4 residues within 4Å: Chain A: V.179, F.180, L.331, M.341 No protein-ligand interaction detected (PLIP) GOL.18: 3 residues within 4Å: Chain B: P.89, E.90, H.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.90, B:E.90, B:H.91, B:H.91 GOL.19: 3 residues within 4Å: Chain B: L.136, G.137, R.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.136, B:R.144 GOL.20: 6 residues within 4Å: Chain B: A.334, R.335, E.338, P.339, M.341 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.339 GOL.21: 5 residues within 4Å: Chain B: V.179, F.180, L.331, M.341 Ligands: GOL.20 No protein-ligand interaction detected (PLIP) GOL.22: 3 residues within 4Å: Chain B: R.186, R.190 Ligands: GOL.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.186, B:R.186, B:R.190 GOL.23: 7 residues within 4Å: Chain B: E.183, R.186, R.187, R.190, D.342, V.346 Ligands: GOL.22 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.183, B:E.183, B:R.186, B:R.187, B:R.190, B:D.342 GOL.24: 2 residues within 4Å: Ligands: DIO.17, GOL.25 No protein-ligand interaction detected (PLIP) GOL.25: 2 residues within 4Å: Chain B: L.228 Ligands: GOL.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.225 Water bridges: B:R.224, B:E.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaefer, C.M. et al., FadA5 a Thiolase from Mycobacterium tuberculosis: A Steroid-Binding Pocket Reveals the Potential for Drug Development against Tuberculosis. Structure (2015)

Release Date

2014-12-17

Peptides

Acetyl-CoA acetyltransferase FadA5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetyl-CoA acetyltransferase FadA5

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