SMTL ID : 5kds.1

ZmpB metallopeptidase in complex with an O-glycopeptide (a2,6-sialylated core-3 pentapeptide).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x THR- ALA- PRO- GLY- GLY: alpha2,6-sialylated core-3 pentapeptide(Non-covalent)

THR-ALA-PRO-GLY-GLY.1: 10 residues within 4Å: Chain A: G.252, A.253, F.254, M.255, H.283, E.284 Ligands: A2G-NAG-SIA.2, A2G-NAG-SIA.2, ZN.3, TLA.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.254, A:F.254 Hydrogen bonds: A:F.254, A:M.255, A:E.284

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

A2G-NAG-SIA.2: 18 residues within 4Å: Chain A: F.254, M.255, N.276, G.278, W.279, G.280, V.281, H.283, E.298, N.302, R.317, Q.321, T.349 Ligands: THR-ALA-PRO-GLY-GLY.1, THR-ALA-PRO-GLY-GLY.1, THR-ALA-PRO-GLY-GLY.1, THR-ALA-PRO-GLY-GLY.1, THR-ALA-PRO-GLY-GLY.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.349 Hydrogen bonds: A:N.302, A:R.317, A:R.317, A:R.317, A:Q.321, A:N.276, A:G.280, A:V.281 Water bridges: A:T.349, A:T.349, A:T.349, A:N.268, A:W.279, A:W.279, A:R.317, A:R.317, A:R.317 Salt bridges: A:R.317

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.283, H.287, E.298 Ligands: THR-ALA-PRO-GLY-GLY.1, TLA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.283, A:H.287, A:E.298, H2O.2

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 8 residues within 4Å: Chain A: M.255, N.256, H.283, H.287, E.298 Ligands: THR-ALA-PRO-GLY-GLY.1, THR-ALA-PRO-GLY-GLY.1, ZN.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.283

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 5 residues within 4Å: Chain A: N.205, K.206, T.207, K.209, Y.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.207, A:Y.210 Salt bridges: A:K.206

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

EDO.6: 8 residues within 4Å: Chain A: A.22, S.23, L.25, T.51, L.53, V.138, R.139, I.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.51, A:I.140 EDO.7: 2 residues within 4Å: Chain A: 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.8: 5 residues within 4Å: Chain A: Y.64, D.66, K.137, V.138, R.139 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.137 Water bridges: A:D.66 EDO.9: 6 residues within 4Å: Chain A: L.82, P.113, D.115, V.116, Q.193, P.266 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.115, A:Q.193 Water bridges: A:Q.193 EDO.10: 4 residues within 4Å: Chain A: D.115, I.117, P.174, K.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.174

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

Related Entries With Identical Sequence