SMTL ID : 6fop.1

Glycoside hydrolase family 81 from Clostridium thermocellum (CtLam81A), Mutant E515A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: L.467, R.468, F.470 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:F.470, H2O.3, H2O.9, H2O.10, H2O.19 CA.2: 6 residues within 4Å: Chain A: D.378, T.381, E.386, K.389 Ligands: CA.3, CL.19 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.378, A:D.378, A:T.381, A:E.386, A:K.389 CA.3: 4 residues within 4Å: Chain A: D.378, E.386 Ligands: CA.2, CL.19 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.386, H2O.7, H2O.22, H2O.22, H2O.23

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 2 residues within 4Å: Chain A: P.16, T.387 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.16, A:T.387 MPD.5: 9 residues within 4Å: Chain A: Y.340, K.344, S.493, E.496, I.576, L.579, W.614, E.641 Ligands: MPD.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.340, A:K.344, A:L.579 Water bridges: A:E.641 MPD.6: 7 residues within 4Å: Chain A: Y.340, Y.407, D.415, F.418, W.565, W.566 Ligands: MPD.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.340, A:Y.407, A:Y.407, A:W.566 Water bridges: A:D.415, A:D.415 MPD.7: 5 residues within 4Å: Chain A: N.308, P.354, E.357, R.433, Y.687 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.687 Hydrogen bonds: A:E.357 Water bridges: A:N.308 MPD.8: 4 residues within 4Å: Chain A: P.15, P.16, T.387, P.404 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.15 MPD.9: 1 residues within 4Å: Chain A: W.565 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.565, A:W.565, A:W.565, A:W.565 Water bridges: A:N.414 MPD.10: 7 residues within 4Å: Chain A: G.33, A.34, Y.393, S.395, G.398, T.462, R.463 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.463 MPD.11: 5 residues within 4Å: Chain A: N.321, L.359, G.360, N.361 Ligands: CL.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.321, A:G.360 MPD.12: 5 residues within 4Å: Chain A: Y.155, C.162, L.214, T.215, K.218 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.155, A:Y.155, A:L.214 MPD.13: 9 residues within 4Å: Chain A: T.237, E.238, S.239, T.667, A.668, D.669, T.697, F.698, S.699 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.238 MPD.14: 4 residues within 4Å: Chain A: K.559, E.563, I.564, W.565 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.565, A:W.565 Hydrogen bonds: A:K.559, A:K.559, A:E.563 MPD.15: 3 residues within 4Å: Chain A: Y.216, P.278, Y.279 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.279

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 4 residues within 4Å: Chain A: Y.155, Q.161, C.162, K.218 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: N.321, N.325 Ligands: MPD.11 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain A: E.253, G.254 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain A: D.378, T.381, K.383, E.386 Ligands: CA.2, CA.3 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.20: 3 residues within 4Å: Chain A: T.569, N.570, C.606 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.570 NA.21: 3 residues within 4Å: Chain A: P.640, S.645, K.646 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.646 Water bridges: A:S.645

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.22: 5 residues within 4Å: Chain A: P.36, I.107, S.108, D.109, F.466 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.36, A:I.107 Hydrogen bonds: A:F.466 ACT.23: 2 residues within 4Å: Chain A: T.387, A.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.387

4 x MG: MAGNESIUM ION(Non-covalent)

MG.24: 6 residues within 4Å: Chain A: Y.26, I.44, N.47, Q.48, Y.49, A.102 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:I.44, A:N.47, A:Q.48, A:Y.49, A:A.102 MG.25: 3 residues within 4Å: Chain A: K.631, N.632, W.634 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.631, A:W.634, H2O.14 MG.26: 1 residues within 4Å: Chain A: K.540 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.540, H2O.9, H2O.22, H2O.24 MG.27: 4 residues within 4Å: Chain A: D.146, F.147, G.188, T.189 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.146, A:F.147, A:G.188, H2O.3, H2O.21

2 x NI: NICKEL (II) ION(Non-covalent)

NI.28: 4 residues within 4Å: Chain A: H.562, H.574, E.601, E.605 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.562, A:H.574, A:E.601, A:E.605, A:E.605 NI.29: 2 residues within 4Å: Chain A: N.635, E.636 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, K. et al., Novel insights into the degradation of beta-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase. Int.J.Biol.Macromol. (2018)

Release Date

2019-03-13

Peptides

Glycoside hydrolase family 81: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycoside hydrolase family 81