SMTL ID : 3iu8.2 (1 other biounit)

M. tuberculosis methionine aminopeptidase with Ni inhibitor T03

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

9 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 5 residues within 4Å: Chain A: D.134, D.145, E.272 Ligands: NI.2, T03.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.134, A:D.134, A:D.145, A:E.272 NI.2: 7 residues within 4Å: Chain A: D.145, H.208, T.239, E.241, E.272 Ligands: NI.1, T03.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.145, A:H.208, A:E.241, A:E.272 NI.3: 3 residues within 4Å: Chain A: H.117 Ligands: T03.4, CL.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.117, H2O.6 NI.8: 5 residues within 4Å: Chain B: D.134, D.145, E.272 Ligands: NI.9, T03.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.134, B:D.134, B:D.145, B:E.272 NI.9: 7 residues within 4Å: Chain B: D.145, H.208, T.239, E.241, E.272 Ligands: NI.8, T03.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.145, B:H.208, B:E.241, B:E.272 NI.10: 3 residues within 4Å: Chain B: H.117 Ligands: T03.11, CL.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.117, H2O.13 NI.15: 5 residues within 4Å: Chain C: D.134, D.145, E.272 Ligands: NI.16, T03.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.134, C:D.134, C:D.145, C:E.272 NI.16: 7 residues within 4Å: Chain C: D.145, H.208, T.239, E.241, E.272 Ligands: NI.15, T03.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.145, C:H.208, C:E.241, C:E.272 NI.17: 3 residues within 4Å: Chain C: H.117 Ligands: T03.18, CL.21 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.117, H2O.19

3 x T03: 3-[(4-fluorobenzyl)sulfanyl]-4H-1,2,4-triazole(Non-covalent)

T03.4: 15 residues within 4Å: Chain A: T.97, Y.100, C.108, H.117, D.134, D.145, H.208, F.214, E.241, W.258, E.272 Ligands: NI.1, NI.2, NI.3, CL.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.100, A:W.258 Water bridges: A:N.147 pi-Stacking: A:H.117 T03.11: 15 residues within 4Å: Chain B: T.97, Y.100, C.108, H.117, D.134, D.145, H.208, F.214, E.241, W.258, E.272 Ligands: NI.8, NI.9, NI.10, CL.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.100, B:W.258 Water bridges: B:N.147 pi-Stacking: B:H.117 T03.18: 15 residues within 4Å: Chain C: T.97, Y.100, C.108, H.117, D.134, D.145, H.208, F.214, E.241, W.258, E.272 Ligands: NI.15, NI.16, NI.17, CL.21 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.100, C:W.258 Water bridges: C:N.147 pi-Stacking: C:H.117

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

SO4.5: 2 residues within 4Å: Chain A: N.23 Chain B: R.203 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.23 Water bridges: A:N.23, A:W.24, B:Y.223 Salt bridges: B:R.203 SO4.12: 2 residues within 4Å: Chain B: N.23 Chain C: R.203 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:Y.223, B:N.23, B:W.24 Salt bridges: C:R.203 Hydrogen bonds: B:N.23 SO4.19: 2 residues within 4Å: Chain A: R.203 Chain C: N.23 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.23 Water bridges: C:N.23, C:W.24, A:Y.223 Salt bridges: A:R.203

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

CL.6: 2 residues within 4Å: Chain A: R.172, R.196 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: H.117 Ligands: NI.3, T03.4 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.172, R.196 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: H.117 Ligands: NI.10, T03.11 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: R.172, R.196 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: H.117 Ligands: NI.17, T03.18 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J.P. et al., Catalysis and Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidase. J.Med.Chem. (2010)

Release Date

2010-01-12

Peptides

Methionine aminopeptidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Methionine aminopeptidase

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