SMTL ID : 4wyg.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis complexed with a fragment hit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: W.85, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 Chain B: G.336, P.337, T.338 Ligands: 3W1.3 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.240, A:I.276, A:K.303 Hydrogen bonds: A:G.144, A:S.145, A:K.303, B:T.338, B:T.338 Water bridges: A:S.145, A:D.180, A:E.240, B:F.339 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.8: 15 residues within 4Å: Chain A: G.336, P.337, T.338 Chain B: W.85, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 Ligands: 3W1.10 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.240, B:I.276, B:K.303 Hydrogen bonds: B:G.144, B:S.145, B:S.145, A:T.338, A:T.338, A:T.338 Water bridges: B:S.145, B:D.180, B:E.240, A:F.339 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 10 residues within 4Å: Chain A: P.44, Y.45, S.47, E.51, W.84, L.405, R.420 Chain B: G.113, G.114 Ligands: 3W1.3 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Water bridges: B:F.112, B:G.114, A:P.44 Hydrogen bonds: A:S.47, A:S.47 Salt bridges: A:E.51, A:E.51, A:R.420 EPE.9: 9 residues within 4Å: Chain A: G.113, G.114 Chain B: P.44, Y.45, E.51, W.84, L.405, R.420 Ligands: 3W1.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:G.114 Salt bridges: B:E.51, B:E.51, B:R.420

3 x 3W1: 1-{4-[(4-chloro-1H-pyrazol-1-yl)methyl]phenyl}methanamine(Non-covalent)

3W1.3: 12 residues within 4Å: Chain A: Y.45, W.84, W.85, Y.177, M.194, A.246, R.420, F.422 Chain B: G.336, T.338 Ligands: PLP.1, EPE.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.45, A:W.85, A:Y.177, A:A.246 Hydrogen bonds: A:Y.45, B:T.338 Water bridges: A:D.180 pi-Stacking: A:F.422 3W1.10: 11 residues within 4Å: Chain A: G.336, T.338 Chain B: Y.45, W.84, W.85, Y.177, M.194, A.246, F.422 Ligands: PLP.8, EPE.9 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.45, B:W.84, B:W.84, B:W.85, B:A.246 pi-Stacking: B:F.422 Hydrogen bonds: A:G.336 3W1.13: 8 residues within 4Å: Chain B: R.213, V.242, F.251, H.252, D.253, P.254, H.291, C.391 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.242, B:P.254

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

EDO.4: 3 residues within 4Å: Chain A: V.242, H.252, C.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.252 Water bridges: A:H.291 EDO.5: 4 residues within 4Å: Chain A: R.213, R.250, F.251, R.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.251 Water bridges: A:R.250 EDO.6: 5 residues within 4Å: Chain A: R.364, I.433, C.434, T.435, P.436 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.433 EDO.7: 4 residues within 4Å: Chain A: A.133, G.293, V.294, S.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.133, A:G.293 EDO.11: 2 residues within 4Å: Chain B: W.65, E.76 No protein-ligand interaction detected (PLIP) EDO.12: 3 residues within 4Å: Chain B: R.174, H.191, P.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.191 Water bridges: B:R.174, B:R.174 EDO.14: 6 residues within 4Å: Chain B: H.43, E.51, V.53, S.54, P.55 Ligands: EDO.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.53 Water bridges: B:L.41, B:S.46, B:E.51 EDO.15: 7 residues within 4Å: Chain B: D.37, G.38, L.41, H.43, I.48, P.55 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.37, B:L.41 Water bridges: B:G.38, B:G.49 EDO.16: 4 residues within 4Å: Chain B: R.174, Q.205, V.206, F.207 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.174, B:Q.205, B:F.207 Water bridges: B:R.169, B:R.174, B:F.207 EDO.17: 3 residues within 4Å: Chain B: R.266, Y.267 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.266, B:Y.267 EDO.18: 3 residues within 4Å: Chain B: R.266, Y.267 Ligands: EDO.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.266, B:Y.267 Water bridges: B:Y.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dai, R. et al., Fragment-Based Exploration of Binding Site Flexibility in Mycobacterium tuberculosis BioA. J.Med.Chem. (2015)

Release Date

2015-07-08

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

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