SMTL ID : 4wyd.1

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase from Mycobacterium tuberculosis complexed with a fragment from DSF screening

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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: 3VR.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.240, A:I.276, A:K.303 Hydrogen bonds: A:G.144, A:S.145, A:S.145, A:Y.177, A:K.303, B:T.338, B:T.338 Water bridges: A:S.145, A:S.145, A:E.240 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.11: 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: 3VR.12 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.240, B:I.276, B:K.303 Hydrogen bonds: B:S.143, B:G.144, B:S.145, A:T.338, A:T.338 Water bridges: B:S.145, B:S.145, B:D.180, B:E.240 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x 3VR: N-methyl-1-[4-(1H-pyrazol-1-ylmethyl)phenyl]methanamine(Non-covalent)

3VR.2: 12 residues within 4Å: Chain A: Y.45, W.84, W.85, Y.177, M.194, A.246, F.422 Chain B: G.336, P.337, T.338 Ligands: PLP.1, EPE.3 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.45, A:W.85, A:Y.177, A:A.246, A:F.422 Hydrogen bonds: A:Y.45, A:Y.177, B:T.338 Water bridges: A:Y.427 3VR.12: 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.11, EPE.13 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.45, B:W.85, B:W.85, B:Y.177, B:A.246, B:F.422 Hydrogen bonds: B:Y.45, B:Y.177, A:T.338

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

EPE.3: 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: 3VR.2 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:G.114 Hydrogen bonds: A:S.47 Salt bridges: A:E.51, A:E.51, A:R.420 EPE.13: 10 residues within 4Å: Chain A: G.113, G.114 Chain B: P.44, Y.45, S.47, E.51, W.84, L.405, R.420 Ligands: 3VR.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.47 Salt bridges: B:E.51, B:E.51, B:R.420 Water bridges: A:G.114

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

EDO.4: 4 residues within 4Å: Chain A: R.213, R.250, F.251, R.389 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.251, A:F.251 Water bridges: A:R.213, A:D.387 EDO.5: 4 residues within 4Å: Chain A: V.242, P.254, H.291, C.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.291 Water bridges: A:G.392 EDO.6: 2 residues within 4Å: Chain A: R.162, L.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.162 EDO.7: 6 residues within 4Å: Chain A: G.375, T.378, T.440, T.443, S.444, V.447 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.375, A:T.378, A:T.443 Water bridges: A:S.444 EDO.8: 2 residues within 4Å: Chain A: R.261, R.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.261 Water bridges: A:R.261, A:R.261 EDO.9: 7 residues within 4Å: Chain A: D.129, I.130, T.131, P.132, A.133, D.290 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.129, A:D.290 EDO.10: 2 residues within 4Å: Chain A: D.290 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.290 EDO.14: 2 residues within 4Å: Chain B: Q.73, I.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.73 Water bridges: B:R.70, B:R.70 EDO.15: 4 residues within 4Å: Chain B: R.213, R.250, F.251, R.389 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.251 Water bridges: B:R.213, B:R.213, B:D.387, B:D.387, B:E.398 EDO.16: 2 residues within 4Å: Chain B: W.65, E.76 No protein-ligand interaction detected (PLIP) EDO.17: 2 residues within 4Å: Chain B: R.213, D.214 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.214 Water bridges: B:R.213, B:D.387

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

2015-07-15

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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