SMTL ID : 3iu7.2 (1 other biounit)

M. tuberculosis methionine aminopeptidase with Mn inhibitor A02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.134, T.136, D.145, E.272 Ligands: MN.2, FCD.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.134, A:D.134, A:D.145, A:E.272, H2O.10 MN.2: 7 residues within 4Å: Chain A: D.145, H.208, T.239, E.241, E.272 Ligands: MN.1, FCD.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.145, A:H.208, A:E.241, A:E.272 MN.7: 6 residues within 4Å: Chain B: D.134, T.136, D.145, E.272 Ligands: MN.8, FCD.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.134, B:D.134, B:D.145, B:E.272, H2O.20 MN.8: 7 residues within 4Å: Chain B: D.145, H.208, T.239, E.241, E.272 Ligands: MN.7, FCD.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.145, B:H.208, B:E.241, B:E.272 MN.13: 6 residues within 4Å: Chain C: D.134, T.136, D.145, E.272 Ligands: MN.14, FCD.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.134, C:D.134, C:D.145, C:E.272, H2O.29 MN.14: 7 residues within 4Å: Chain C: D.145, H.208, T.239, E.241, E.272 Ligands: MN.13, FCD.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.145, C:H.208, C:E.241, C:E.272

6 x FCD: 5-(2-CHLOROPHENYL)FURAN-2-CARBOXYLIC ACID(Non-covalent)

FCD.3: 15 residues within 4Å: Chain A: T.97, Y.100, F.103, C.108, H.117, D.134, D.145, H.208, F.214, H.215, E.241, W.258, E.272 Ligands: MN.1, MN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.258 Salt bridges: A:H.208, A:H.215 pi-Stacking: A:Y.100 pi-Cation interactions: A:H.117 FCD.4: 9 residues within 4Å: Chain A: T.146, N.147, A.148, R.167, T.170, M.171, F.271, E.272, H.273 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.148, A:R.167, A:F.271 pi-Stacking: A:H.273 pi-Cation interactions: A:R.167 FCD.9: 15 residues within 4Å: Chain B: T.97, Y.100, F.103, C.108, H.117, D.134, D.145, H.208, F.214, H.215, E.241, W.258, E.272 Ligands: MN.7, MN.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.258 Salt bridges: B:H.208, B:H.215 pi-Stacking: B:Y.100 pi-Cation interactions: B:H.117 FCD.10: 9 residues within 4Å: Chain B: T.146, N.147, A.148, R.167, T.170, M.171, F.271, E.272, H.273 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.148, B:R.167, B:F.271 pi-Stacking: B:H.273 pi-Cation interactions: B:R.167 FCD.15: 15 residues within 4Å: Chain C: T.97, Y.100, F.103, C.108, H.117, D.134, D.145, H.208, F.214, H.215, E.241, W.258, E.272 Ligands: MN.13, MN.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.258 Salt bridges: C:H.208, C:H.215 pi-Stacking: C:Y.100 pi-Cation interactions: C:H.117 FCD.16: 9 residues within 4Å: Chain C: T.146, N.147, A.148, R.167, T.170, M.171, F.271, E.272, H.273 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.148, C:R.167, C:F.271 pi-Stacking: C:H.273 pi-Cation interactions: C:R.167

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

SO4.5: 2 residues within 4Å: Chain A: R.203 Chain B: N.23 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.23 Water bridges: B:N.23, B:W.24, A:D.204, A:D.204, A:D.204 Salt bridges: A:R.203 SO4.11: 2 residues within 4Å: Chain B: R.203 Chain C: N.23 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Water bridges: B:D.204, B:D.204, B:D.204, C:N.23, C:W.24 Salt bridges: B:R.203 Hydrogen bonds: C:N.23 SO4.17: 2 residues within 4Å: Chain A: N.23 Chain C: R.203 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:D.204, C:D.204, C:D.204, A:N.23, A:W.24 Salt bridges: C:R.203 Hydrogen bonds: A:N.23

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

CL.6: 2 residues within 4Å: Chain A: R.172, R.196 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.172, R.196 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: R.172, R.196 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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