SMTL ID : 5kdu.1

ZmpB metallopeptidase in complex with a2,6-Sialyl T-antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x A2G- GAL- SIA: beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose

A2G-GAL-SIA.1: 16 residues within 4Å: Chain A: F.254, M.255, N.268, N.276, G.278, W.279, G.280, V.281, H.283, E.298, N.302, R.317, T.349 Ligands: EDO.6, EDO.9, SER.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.349 Hydrogen bonds: A:N.302, A:R.317, A:R.317, A:R.317, A:N.268, A:N.276, A:G.278, A:W.279, A:G.280, A:V.281 Water bridges: A:E.298 Salt bridges: A:R.317

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

EDO.2: 3 residues within 4Å: Chain A: Y.64, G.96, K.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.97 Water bridges: A:P.95, A:K.97 EDO.3: 6 residues within 4Å: Chain A: Y.361, L.362, N.365, A.440, M.441, N.442 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.442 Water bridges: A:Y.363, A:N.365, A:N.365 EDO.4: 7 residues within 4Å: Chain A: A.22, S.23, L.25, T.51, V.138, R.139, I.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.51, A:I.140 EDO.5: 4 residues within 4Å: Chain A: K.206, T.207, K.209, Y.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.207, A:Y.210 EDO.6: 5 residues within 4Å: Chain A: R.317, Q.321, T.349 Ligands: A2G-GAL-SIA.1, A2G-GAL-SIA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.317, A:Q.321, A:T.349 Water bridges: A:T.349 EDO.7: 4 residues within 4Å: Chain A: V.24, Y.64, D.66, K.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137 EDO.8: 8 residues within 4Å: Chain A: K.41, V.42, W.43, H.287, N.288, D.290, G.292, T.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.288 Water bridges: A:T.295 EDO.9: 5 residues within 4Å: Chain A: N.268, D.270, A.271, N.276 Ligands: A2G-GAL-SIA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.268, A:N.268 Water bridges: A:N.276 EDO.10: 4 residues within 4Å: Chain A: T.295, I.296, V.297, I.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.297

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 4 residues within 4Å: Chain A: H.283, H.287, E.298 Ligands: SER.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.283, A:H.287, A:E.298

1 x SER: SERINE(Non-covalent)

SER.12: 7 residues within 4Å: Chain A: A.253, F.254, M.255, H.283, E.284 Ligands: A2G-GAL-SIA.1, ZN.11 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Water bridges: S.12, A:E.298 Hydrogen bonds: A:F.254, A:M.255, A:E.284

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

F5/8 type C domain protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F5/8 type C domain protein

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