SMTL ID : 5ecu.1

The unliganded structure of Caldicellulosiruptor saccharolyticus GH5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: H.54, S.263, G.264, W.290, K.295, E.297, S.299 Ligands: EDO.14, EDO.20, GOL.26 Ligand excluded by PLIP EDO.2: 7 residues within 4Å: Chain A: R.26, L.27, F.150, I.152, I.153, N.195, I.196 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: N.73, N.111 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: D.74, R.336, K.340 Ligands: GOL.28 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: V.309, S.310, L.351 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: E.182, I.185, K.186, I.216, A.217 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: R.35, R.36, I.37, M.222, I.246, V.250, P.251, V.252, I.285 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.189, G.192, N.193, E.194 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: S.22, I.109, D.112, F.150, H.151 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: F.59, Q.61, N.294 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: E.278, Y.279, A.282 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: V.23, D.40, N.42 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: V.234, D.235, K.243, Y.279 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: Y.228, E.256, A.262, S.263, G.264, W.290 Ligands: EDO.1, CA.43 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: N.15, S.16, V.18, K.19 Ligands: EDO.21 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain A: M.187, Q.190, M.191 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: N.169, R.207, Y.237, N.241 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: E.348, R.349, T.350, L.351 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: G.87, E.88, N.123, P.124 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: W.58, K.295 Ligands: EDO.1, GOL.26 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: V.18, K.19, K.20, V.23 Ligands: EDO.15 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: I.29, I.30, K.31, R.36, D.219 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: R.336, S.337, I.342, P.343, Y.344, Q.345 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: R.36, A.211, I.212, P.215, G.249, V.250, P.251 Ligands: ACT.40 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: E.103, K.106, L.107, Q.110 Ligand excluded by PLIP

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 8 residues within 4Å: Chain A: H.54, W.58, Y.85, W.290, K.295, E.297 Ligands: EDO.1, EDO.20 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.85, A:W.290, A:K.295, A:K.295 Water bridges: A:E.88, A:E.297 GOL.27: 3 residues within 4Å: Chain A: D.209, I.212, K.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.207, A:D.209 GOL.28: 4 residues within 4Å: Chain A: D.74, R.336, K.340 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.74, A:R.336, A:K.340 Water bridges: A:K.340 GOL.29: 5 residues within 4Å: Chain A: Q.311, A.312, T.313, D.314, E.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.311, A:D.314, A:E.327 GOL.30: 3 residues within 4Å: Chain A: K.175, K.213, D.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.175, A:K.175 GOL.31: 8 residues within 4Å: Chain A: P.127, N.128, A.129, Y.132, K.133, A.135, K.136, Y.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.127, A:A.135, A:K.136 Water bridges: A:D.137 GOL.32: 6 residues within 4Å: Chain A: N.15, K.20, A.72, N.73, G.76, K.340 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.20, A:K.340

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.33: 6 residues within 4Å: Chain A: V.303, P.304, I.306, S.329, I.330, R.349 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.303 Hydrogen bonds: A:I.330 Water bridges: A:S.329, A:S.331, A:R.349, A:R.349 Salt bridges: A:R.349 MLI.34: 3 residues within 4Å: Chain A: P.162, T.163, D.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.164 MLI.35: 4 residues within 4Å: Chain A: D.271, Y.344, P.346 Ligands: ACT.36 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.344 Water bridges: A:D.271, A:D.274, A:Y.344

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

ACT.36: 6 residues within 4Å: Chain A: Y.4, L.270, D.271, D.274, Y.344 Ligands: MLI.35 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.270, A:Y.344 Hydrogen bonds: A:Y.4, A:D.271 Water bridges: A:D.274 ACT.37: 3 residues within 4Å: Chain A: N.128, K.176, A.179 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.128, A:N.128 ACT.38: 4 residues within 4Å: Chain A: Q.32, P.45, N.284 Ligands: ACT.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.32, A:N.284 ACT.39: 6 residues within 4Å: Chain A: H.11, L.17, N.281, A.282, N.284 Ligands: ACT.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.282, A:N.284 Water bridges: A:N.284 ACT.40: 4 residues within 4Å: Chain A: I.216, D.218, D.219 Ligands: EDO.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.218 Water bridges: A:R.36 ACT.41: 3 residues within 4Å: Chain A: S.319, D.320, Q.321 No protein-ligand interaction detected (PLIP) ACT.42: 8 residues within 4Å: Chain A: I.86, Y.91, A.92, W.119, I.131, Y.132, K.133, G.134 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.86, A:Y.91, A:A.92 Hydrogen bonds: A:G.134

2 x CA: CALCIUM ION(Non-covalent)

CA.43: 4 residues within 4Å: Chain A: E.159, Y.228, E.256 Ligands: EDO.14 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.159, A:E.256, H2O.3, H2O.4, H2O.12 CA.44: 1 residues within 4Å: Chain A: I.63 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:I.63, H2O.3, H2O.8, H2O.9, H2O.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alahuhta, P.M. et al., The structure of Caldicellulosiruptor saccharolyticus GH5. To Be Published

Release Date

2016-11-02

Peptides

Cellulase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cellulase