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

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ZINC METALLOPROTEASE ZMP1 IN COMPLEX WITH INHIBITOR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.529, H.533, E.596, H.658 Ligands: RDF.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.529, A:H.533, A:E.596, A:E.596, RDF.2

1 x RDF: N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN(Non-covalent)

RDF.2: 20 residues within 4Å: Chain A: F.84, M.482, V.487, N.488, A.489, Y.490, V.526, H.529, E.530, H.533, E.596, W.640, R.652, P.657, H.658, R.664 Ligands: ZN.1, 211.3, PGE.21, ACT.26 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.84, A:F.84, A:V.526, A:W.640, A:P.657 Hydrogen bonds: A:V.487, A:N.488, A:N.488, A:N.488, A:R.664, A:R.664 Water bridges: A:R.652, A:D.656 Salt bridges: A:H.658, A:H.658 pi-Stacking: A:F.84

1 x 211: 2,2',2''-NITRILOTRIETHANOL(Non-covalent)

211.3: 5 residues within 4Å: Chain A: R.651, R.652, D.656, H.658 Ligands: RDF.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.651, A:R.651, A:R.652 Salt bridges: A:D.656

15 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: P.42, S.43, G.44, D.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.43, A:G.44 PEG.5: 7 residues within 4Å: Chain A: F.88, A.91, V.365, E.369, Q.485, T.486, V.487 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.366 PEG.6: 8 residues within 4Å: Chain A: S.122, V.129, P.136, W.334, D.450, D.451, L.452, Y.453 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.122, A:W.334, A:L.452 PEG.7: 3 residues within 4Å: Chain A: T.111, D.112, A.113 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.112, A:A.113 Water bridges: A:D.112, A:R.115 PEG.8: 4 residues within 4Å: Chain A: Y.262, N.263, L.264, R.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.264, A:R.265 PEG.9: 5 residues within 4Å: Chain A: Y.676, Q.677, D.680, V.681 Ligands: PGE.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.677 PEG.10: 4 residues within 4Å: Chain A: I.41, D.515, E.516, P.621 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain A: R.162, K.444, D.465 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.444, A:K.444 PEG.12: 5 residues within 4Å: Chain A: Y.172, T.188, R.255, R.299, Q.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.255, A:R.299, A:R.299, A:Q.300 Water bridges: A:Q.189 PEG.13: 8 residues within 4Å: Chain A: A.649, R.652, L.653, D.656, H.658, S.659, P.660, P.661 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.652, A:D.656 Water bridges: A:D.656, A:D.656 PEG.14: 3 residues within 4Å: Chain A: D.394, D.398, A.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.394, A:A.431, A:A.431 PEG.15: 7 residues within 4Å: Chain A: D.53, A.54, R.55, D.58, D.59 Ligands: PEG.17, ACT.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.55, A:D.58, A:D.59 PEG.16: 4 residues within 4Å: Chain A: A.566, E.569, Q.570, R.693 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.569, A:Q.570, A:R.693 PEG.17: 3 residues within 4Å: Chain A: D.58, R.577 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.58 PEG.18: 5 residues within 4Å: Chain A: N.399, A.610, L.613, S.614, N.616 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.610, A:N.616

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.19: 3 residues within 4Å: Chain A: I.406, E.410, L.609 No protein-ligand interaction detected (PLIP) PGE.20: 5 residues within 4Å: Chain A: D.673, Y.676, Q.677, R.694 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.694, A:R.694 PGE.21: 9 residues within 4Å: Chain A: Y.490, Y.491, P.493, E.530, H.533, D.536, Q.538, G.539 Ligands: RDF.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.491, A:E.530 Water bridges: A:H.533 PGE.22: 4 residues within 4Å: Chain A: I.74, Q.355, K.643, R.645 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.74, A:Q.355, A:R.645 PGE.23: 6 residues within 4Å: Chain A: A.52, R.55, P.56, H.63, L.626, Q.630 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.24: 7 residues within 4Å: Chain A: H.49, R.67, W.68, E.71, H.72, D.81, S.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.67, A:E.71

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.25: 4 residues within 4Å: Chain A: D.51, G.66, R.577 Ligands: PEG.15 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.577 ACT.26: 2 residues within 4Å: Chain A: F.481 Ligands: RDF.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.481 ACT.27: 4 residues within 4Å: Chain A: D.537, W.552, R.557, F.560 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.560 Water bridges: A:D.550 Salt bridges: A:R.557 ACT.28: 2 residues within 4Å: Chain A: A.40, I.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.41 Water bridges: A:V.622 ACT.29: 4 residues within 4Å: Chain A: Q.161, V.165, G.170, V.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.161, A:V.171, A:V.171

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

SO4.30: 6 residues within 4Å: Chain A: H.572, H.587, V.588, Q.589, G.590, A.591 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.590, A:A.591 Salt bridges: A:H.572, A:H.587 SO4.31: 4 residues within 4Å: Chain A: R.78, A.79, T.80, R.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.79, A:T.80 Salt bridges: A:R.85

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

CL.32: 3 residues within 4Å: Chain A: R.182, Y.183, L.471 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferraris, D.M. et al., Crystal Structure of Mycobacterium Tuberculosis Zinc-Dependent Metalloprotease-1 (Zmp1), a Metalloprotease Involved in Pathogenicity. J.Biol.Chem. (2011)

Release Date

2011-08-03

Peptides

ENDOPEPTIDASE, PEPTIDASE FAMILY M13: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDOPEPTIDASE, PEPTIDASE FAMILY M13

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