SMTL ID : 5kdx.2 (1 other biounit)

IMPa metallopeptidase in complex with T-antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x A2G- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G-GAL.1: 10 residues within 4Å: Chain A: W.645, W.652, G.653, H.656, Q.680, R.702, Y.736, N.739 Ligands: PO4.3, SER.17 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.736 Hydrogen bonds: A:Q.680, A:R.702, A:R.702, A:R.702

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: Q.33, D.71, N.72, G.328, T.329, T.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.33, A:D.71, A:N.72, A:G.328, A:T.330, A:T.330 PO4.3: 4 residues within 4Å: Chain A: W.652, D.699, R.702 Ligands: A2G-GAL.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.652, A:D.699 Salt bridges: A:R.702 PO4.4: 4 residues within 4Å: Chain A: R.243, P.245, S.246, S.247 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.246, A:S.246, A:S.247 Water bridges: A:R.243, A:R.243 Salt bridges: A:R.243

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: H.656, E.657, H.660, E.676, N.679 Ligands: SER.17 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.656, A:H.660, A:E.676, A:E.676, H2O.1

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

EDO.6: 9 residues within 4Å: Chain A: L.313, Y.316, N.317, Q.321, N.322, L.323, G.370, Y.371, V.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.323, A:Y.371, A:V.372 EDO.7: 10 residues within 4Å: Chain A: Y.371, L.441, N.442, L.463, K.464, S.465, S.480, Y.482, G.483, G.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.371, A:N.442, A:S.480 EDO.8: 8 residues within 4Å: Chain A: G.440, L.441, N.442, K.464, S.465, P.466, D.467, Q.487 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.465, A:D.467 Water bridges: A:K.464, A:K.464 EDO.9: 3 residues within 4Å: Chain A: T.584, Q.593, T.596 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.593 EDO.10: 3 residues within 4Å: Chain A: Q.456, Q.628, Y.629 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.456, A:Q.628, A:Y.629 EDO.11: 8 residues within 4Å: Chain A: L.722, R.826, F.829, A.830, I.834, R.835, T.836, Q.841 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.836, A:Q.841 EDO.12: 4 residues within 4Å: Chain A: T.291, K.352, N.453, T.454 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.352, A:T.454, A:T.454 Water bridges: A:N.453, A:N.453 EDO.13: 6 residues within 4Å: Chain A: S.436, L.437, K.469, V.489, Y.490, S.491 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.469, A:K.469 Water bridges: A:Y.490 EDO.14: 3 residues within 4Å: Chain A: W.214, Y.234, W.239 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: D.755, Y.857, V.868, L.870 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.755, A:D.755, A:L.870, A:L.870 EDO.16: 3 residues within 4Å: Chain A: A.265, Q.269, R.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.265, A:R.305, A:R.305

1 x SER: SERINE(Non-covalent)

SER.17: 5 residues within 4Å: Chain A: H.656, E.657, Y.736 Ligands: A2G-GAL.1, ZN.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:G.635, A:E.657, S.17, S.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noach, I. et al., Recognition of protein-linked glycans as a determinant of peptidase activity. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-01-11

Peptides

Metallopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Metallopeptidase

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