SMTL ID : 8jt1.2 (1 other biounit)

COLLAGENASE FROM GRIMONTIA (VIBRIO) HOLLISAE 1706B COMPLEXED WITH GLY-PRO-HYP-GLY-PRO-HYP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

3 x GLY- PRO- HYP- GLY- PRO- HYP: 6-mer peptide(Non-covalent)

GLY-PRO-HYP-GLY-PRO-HYP.1: 19 residues within 4Å: Chain A: N.368, G.369, G.370, M.371, Y.372, W.401, N.402, H.405, E.406, H.409, F.421, E.433, Y.468, F.471, V.473, Y.477 Ligands: ZN.4, EDO.32, EDO.35 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.368, A:Y.477 Hydrogen bonds: A:G.369, A:G.370, A:Y.372, A:N.402, A:Y.477 Water bridges: A:N.368 GLY-PRO-HYP-GLY-PRO-HYP.2: 14 residues within 4Å: Chain A: N.31, F.34, L.77, R.80, Y.83, Y.84, F.87, Y.88, E.128, I.131, D.134, S.135, T.172 Ligands: EDO.49 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:F.87, A:I.131 Hydrogen bonds: A:R.80, A:R.80, A:Y.88, A:E.128, A:D.134 Water bridges: A:N.127, A:D.134 GLY-PRO-HYP-GLY-PRO-HYP.3: 6 residues within 4Å: Chain A: F.171, F.175, N.217, R.220, E.221, R.224 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.175, A:F.175 Hydrogen bonds: A:N.217, A:N.217, A:E.221, A:R.224, A:R.224 Water bridges: A:N.168

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: H.405, H.409, E.433, Y.477 Ligands: GLY-PRO-HYP-GLY-PRO-HYP.1, GLY-PRO-HYP-GLY-PRO-HYP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.405, A:H.409, A:E.433, H2O.12

4 x CA: CALCIUM ION(Non-covalent)

CA.5: 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.3, H2O.4 CA.6: 3 residues within 4Å: Chain A: D.304, N.349, E.390 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.304, A:E.390, H2O.2, H2O.3, H2O.3 CA.7: 3 residues within 4Å: Chain A: T.451, D.454, S.456 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.451, A:D.454, A:S.456, A:S.456, H2O.2 CA.8: 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

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

EDO.9: 7 residues within 4Å: Chain A: W.153, N.154, A.158, D.203, T.205, K.206, T.211 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Y.64, A.65, G.66, G.68 Ligands: EDO.27 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Q.309, E.390, A.391, S.392, F.399 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: G.455, S.456, T.457 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.506, W.507, A.508, E.509 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: F.421, G.422, P.424, E.426, L.427 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: D.107, V.110, Q.111, A.141 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: A.461, F.464, D.465, K.511, I.514, S.515, A.518 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: N.180, Q.182 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: D.144, T.147, Q.148, A.192 Ligands: EDO.33 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: E.159, W.161, R.164 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain A: E.426 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: T.184, S.185, I.187, G.188, A.231 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: T.352, D.353, K.356, Y.357 Ligands: EDO.53 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: F.34, Q.41, Y.84, Y.88 Ligands: EDO.24 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain A: Y.88, N.89, S.90 Ligands: EDO.23 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain A: E.42 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: S.46, S.47, N.48 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: S.69, D.70, E.71 Ligands: EDO.10 Ligand excluded by PLIP EDO.28: 3 residues within 4Å: Chain A: D.351, T.366, N.368 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain A: G.359, I.364 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: A.336, Y.418, Q.504 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: T.327, L.328, E.329, P.492, V.495, Q.496, L.499 Ligands: TRS.55 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: Y.372, H.409, D.412, G.413, M.417, S.432 Ligands: GLY-PRO-HYP-GLY-PRO-HYP.1, EDO.36 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain A: Y.116, D.144, V.145, Q.148 Ligands: EDO.18 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain A: S.295, T.297, I.298, E.321 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: L.373, E.374, G.375, F.421 Ligands: GLY-PRO-HYP-GLY-PRO-HYP.1 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: M.417, F.421, P.424, V.428 Ligands: EDO.32 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain A: G.68, S.69, D.70, E.73, A.121, K.124, V.125 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain A: L.174, Q.178, Y.183, R.224, L.225, R.227, Y.228 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain A: Q.447, T.451, D.474, R.478 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain A: Q.520, Y.521, E.524 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain A: T.457, Y.458, T.459, W.479, Q.522, F.525, A.526, T.529 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain A: T.242, F.245, G.246, F.274, N.275, I.276 Ligands: EDO.43 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain A: F.245, Y.248, P.249, S.250, W.258 Ligands: EDO.42 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain A: E.494, G.516, W.517, Q.520, Y.521 Ligand excluded by PLIP EDO.45: 3 residues within 4Å: Chain A: Q.496, S.500, R.503 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain A: W.161, Y.162 Ligand excluded by PLIP EDO.47: 1 residues within 4Å: Chain A: T.151 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain A: A.113, H.114, D.117 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain A: D.134, T.172, F.175, G.176 Ligands: GLY-PRO-HYP-GLY-PRO-HYP.2, GLY-PRO-HYP-GLY-PRO-HYP.2 Ligand excluded by PLIP EDO.50: 3 residues within 4Å: Chain A: Y.468, D.469, G.470 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain A: R.441, V.442, N.443, D.444 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain A: N.127, I.131, N.165, N.168, G.169 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain A: Y.251, G.252, D.255, K.356, Y.357 Ligands: EDO.22 Ligand excluded by PLIP

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

PEG.54: 5 residues within 4Å: Chain A: W.161, R.164, N.165, P.210, F.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.164, A:N.165

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.55: 3 residues within 4Å: Chain A: E.329, Q.496 Ligands: EDO.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.492, A:Q.496, A:Q.496

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ueshima, S. et al., Insights into the catalytic mechanism of Grimontia hollisae collagenase through structural and mutational analyses. Febs Lett. (2023)

Release Date

2024-02-07

Peptides

Microbial collagenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Microbial collagenase

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