SMTL ID : 7sf4.1 (1 other biounit)

M. tb EgtD in complex with imatinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

1 x XDK: 2-AMINO-4-PYRIDYL-PYRIMIDINE(Non-covalent)

XDK.1: 12 residues within 4Å: Chain A: I.50, Y.56, G.161, S.162, T.163, N.166, Y.206, T.213, F.216, M.252, E.282, S.284 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.216 Hydrogen bonds: A:T.163 Salt bridges: A:E.282

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: E.84, L.85, S.90, K.92, V.158, L.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.90, A:V.158, A:L.160 Water bridges: A:S.87 GOL.3: 3 residues within 4Å: Chain A: R.78, R.103, S.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.74, A:R.103, A:S.105 GOL.4: 6 residues within 4Å: Chain A: P.35, F.142, T.163, N.166, L.167 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.35, A:Y.39 GOL.10: 5 residues within 4Å: Chain A: A.17, K.36, W.37, V.114, D.141 No protein-ligand interaction detected (PLIP)

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

EDO.5: 4 residues within 4Å: Chain A: R.69, E.72, R.305, W.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.69, A:R.305 Water bridges: A:R.69 EDO.6: 4 residues within 4Å: Chain A: E.72, S.75, A.76, R.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.72, A:R.305 EDO.7: 6 residues within 4Å: Chain A: E.64, A.68, R.69, T.308, D.309, E.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.64, A:T.308 Water bridges: A:E.64 EDO.8: 5 residues within 4Å: Chain A: K.36, D.141, F.142, E.143 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.142, A:E.143 EDO.9: 5 residues within 4Å: Chain A: G.14, H.15, L.18, W.37, E.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.15 EDO.11: 2 residues within 4Å: Chain A: S.4, N.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.4, A:N.136 Water bridges: A:S.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sudasinghe, T.D. et al., Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production. Sci Rep (2021)

Release Date

2021-12-01

Peptides

Histidine N-alpha-methyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histidine N-alpha-methyltransferase

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