SMTL ID : 3pke.1 (1 other biounit)

M. tuberculosis MetAP with bengamide analog Y10, in Ni form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x Y10: (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide(Non-covalent)

Y10.1: 20 residues within 4Å: Chain A: Y.97, C.105, C.113, H.114, D.131, T.133, D.142, D.201, F.202, T.203, H.205, F.211, H.212, V.216, E.238, M.240, W.255, E.269 Ligands: NI.2, NI.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.97, A:Y.97, A:F.211, A:F.211, A:V.216, A:W.255 Hydrogen bonds: A:T.133, A:D.142, A:T.203 Water bridges: A:Q.267, A:Q.267

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

NI.2: 7 residues within 4Å: Chain A: D.142, H.205, T.236, E.238, E.269 Ligands: Y10.1, NI.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.142, A:H.205, A:E.238, A:E.269 NI.3: 6 residues within 4Å: Chain A: D.131, D.142, E.238, E.269 Ligands: Y10.1, NI.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.131, A:D.131, A:D.142, A:E.269

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

CL.4: 2 residues within 4Å: Chain A: R.169, R.193 Ligand excluded by PLIP

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

SO4.5: 1 residues within 4Å: Chain A: N.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, J.P. et al., Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives. Chemmedchem (2011)

Release Date

2011-04-20

Peptides

Methionine aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine aminopeptidase

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