SMTL ID : 7xeb.1 (1 other biounit)

Collagenase from Grimontia (Vibrio) hollisae 1706B complexed with Gly-Pro-Hyp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

monomer

Ligands

2 x GLY- PRO- HYP: GLY-PRO-HYP peptide(Non-covalent)

GLY-PRO-HYP.1: 15 residues within 4Å: Chain A: N.368, G.370, M.371, Y.372, L.373, E.406, H.409, F.421, E.433, Y.468, F.471, Y.477 Ligands: GLY-PRO-HYP.2, ZN.5, EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.368 Hydrogen bonds: A:G.370, A:Y.372 Salt bridges: A:H.405, A:H.409 GLY-PRO-HYP.2: 13 residues within 4Å: Chain A: N.367, N.368, G.369, G.370, W.401, N.402, H.405, E.406, E.437, F.471, Y.477 Ligands: GLY-PRO-HYP.1, ZN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.477 Hydrogen bonds: A:G.369, A:G.369, A:N.402 Water bridges: A:N.367, A:N.368, A:Y.389, A:W.401

2 x GLY- PRO- HYP- GLY- PRO- HYP: GLY-PRO-HYP-GLY-PRO-HYP peptide(Non-covalent)

GLY-PRO-HYP-GLY-PRO-HYP.3: 11 residues within 4Å: Chain A: N.31, F.34, R.80, Y.83, Y.84, F.87, E.128, I.131, D.134, S.135, T.172 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.34, A:F.87, A:I.131 Hydrogen bonds: A:R.80, A:R.80, A:Y.88, A:E.128 Water bridges: A:N.127 GLY-PRO-HYP-GLY-PRO-HYP.4: 8 residues within 4Å: Chain A: F.171, F.175, N.217, E.221, R.224, D.263, Y.267, Y.268 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.175, A:F.175 Hydrogen bonds: A:N.217, A:N.217, A:R.224, A:R.224, A:D.263

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: H.405, H.409, E.433, Y.477 Ligands: GLY-PRO-HYP.1, GLY-PRO-HYP.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.405, A:H.409, A:E.433, A:E.433

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.374, G.413, M.417, Y.418, G.419 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.374, A:G.413, A:M.417, A:G.419, H2O.1, H2O.2 CA.7: 3 residues within 4Å: Chain A: D.304, N.349, E.390 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.304, A:E.390, A:E.390, H2O.3, H2O.4 CA.8: 3 residues within 4Å: Chain A: T.451, D.454, S.456 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.451, A:T.451, A:D.454, A:S.456, A:S.456 CA.9: 4 residues within 4Å: Chain A: E.86, N.89, S.90, I.92 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.86, A:N.89, A:I.92

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

EDO.10: 3 residues within 4Å: Chain A: A.155, Q.156, E.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.155 Water bridges: A:E.159 EDO.11: 1 residues within 4Å: Chain A: W.161 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: W.153, N.154, A.155, A.158, T.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.153, A:T.211 EDO.13: 6 residues within 4Å: Chain A: Y.372, L.373, E.374, F.421 Ligands: GLY-PRO-HYP.1, GLY-PRO-HYP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.372, A:E.374 Water bridges: A:G.375, A:F.421 EDO.14: 5 residues within 4Å: Chain A: F.245, G.246, Y.248, P.249, W.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ikeuchi, T. et al., Crystal structure of Grimontia hollisae collagenase provides insights into its novel substrate specificity toward collagen. J.Biol.Chem. (2022)

Release Date

2022-06-29

Peptides

Microbial collagenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Microbial collagenase

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