SMTL ID : 4w1w.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with 7-(diethylamino)-3-(thiophene-2-carbonyl)-2H-chromen-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: S.116, G.117, S.118, Y.150, H.151, G.152, E.213, D.247, I.249, A.250, K.276 Chain B: P.310, T.311 18 PLIP interactions: 2 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:T.311, B:T.311, A:G.117, A:S.118, A:K.276 Hydrophobic interactions: A:E.213, A:I.249, A:K.276 Water bridges: A:D.115, A:S.116, A:S.118, A:S.118, A:Y.150, A:Y.150, A:D.153, A:E.213, A:K.276 pi-Stacking: A:Y.150 PLP.8: 13 residues within 4Å: Chain A: P.310, T.311 Chain B: S.116, G.117, S.118, Y.150, H.151, G.152, E.213, D.247, I.249, A.250, K.276 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.150, B:E.213, B:I.249 Hydrogen bonds: B:G.117, B:S.118, B:S.118, A:T.311, A:T.311, A:T.311 Water bridges: B:S.116, B:S.118, B:Y.150, B:D.153, B:E.213 Salt bridges: B:K.276 pi-Stacking: B:Y.150

2 x 3G8: 7-(diethylamino)-3-(thiophen-2-ylcarbonyl)-2H-chromen-2-one(Non-covalent)

3G8.2: 11 residues within 4Å: Chain A: P.17, Y.18, W.57, Y.150, G.165, R.393 Chain B: M.84, G.86, G.309, P.310, T.311 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.17, A:P.17, A:Y.18, A:W.57 Hydrogen bonds: A:R.393 Salt bridges: A:R.393 pi-Stacking: A:Y.18, A:W.57 3G8.9: 12 residues within 4Å: Chain A: M.84, G.86, G.309, P.310, T.311 Chain B: P.17, Y.18, W.57, Y.150, G.165, G.166, R.393 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.17, B:Y.18, B:Y.18, B:W.57 pi-Stacking: B:Y.18, B:W.57

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

EDO.3: 3 residues within 4Å: Chain A: P.227, H.264, A.265 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: P.227, H.264 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.264 EDO.5: 5 residues within 4Å: Chain A: R.147, F.180, A.181, P.182, Q.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.180, A:Q.199 Water bridges: A:R.147 EDO.6: 7 residues within 4Å: Chain A: S.193, A.194, E.197, D.232, D.235, I.236, R.239 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.197, A:E.197, A:D.232, A:D.235, A:R.239 Water bridges: A:A.194 EDO.7: 5 residues within 4Å: Chain A: R.337, I.406, C.407, T.408, P.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.406 Water bridges: A:R.337 EDO.11: 3 residues within 4Å: Chain B: V.215, H.225, P.227 No protein-ligand interaction detected (PLIP) EDO.12: 7 residues within 4Å: Chain B: V.101, D.102, T.104, P.105, A.106, G.107, L.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.102, B:G.107, B:L.108, B:L.108 EDO.13: 2 residues within 4Å: Chain B: W.38, E.49 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 3 residues within 4Å: Chain B: R.234, V.267, S.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, S.W. et al., Target-Based Identification of Whole-Cell Active Inhibitors of Biotin Biosynthesis in Mycobacterium tuberculosis. Chem.Biol. (2015)

Release Date

2015-02-04

Peptides

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase