SMTL ID : 8xis.1

Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: R.486, W.622, H.817, Q.874, S.889, G.890, T.891 Ligands: BGC.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.874, A:G.890 Water bridges: A:R.486, A:R.486, A:H.817, A:S.889, A:T.891 Salt bridges: A:R.486, A:H.817 PO4.19: 8 residues within 4Å: Chain B: R.486, W.622, H.817, Q.874, S.889, G.890, T.891 Ligands: BGC.20 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Q.874, B:S.889, B:G.890 Water bridges: B:R.486, B:R.486, B:H.817, B:H.817, B:L.888, B:S.889 Salt bridges: B:R.486, B:H.817

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.2: 6 residues within 4Å: Chain A: R.486, E.502, W.622, D.624, Q.874 Ligands: PO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.502 Water bridges: A:R.486, A:R.496, A:E.502, A:W.622, A:Q.874 BGC.20: 8 residues within 4Å: Chain B: R.486, R.496, R.501, E.502, W.622, D.624, Q.874 Ligands: PO4.19 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.496, B:E.502 Water bridges: B:R.486, B:E.502, B:E.502, B:D.624, B:D.624, B:Q.874

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: H.292, F.295 Chain B: H.292, F.295 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.292, A:H.292 GOL.8: 9 residues within 4Å: Chain A: D.125, E.127, S.228, S.229, R.231, I.447, E.451, R.472, R.870 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.125, A:S.229, A:R.231, A:R.231 Water bridges: A:E.127, A:S.229, A:S.229, A:R.472, A:R.870 GOL.9: 9 residues within 4Å: Chain A: Y.456, Y.511, R.566, L.897, I.900, S.901, I.905, E.906, Y.907 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.511, A:Y.511, A:R.566, A:Y.907 Water bridges: A:R.566, A:S.901 GOL.16: 6 residues within 4Å: Chain A: A.843, R.844, Y.847, R.919, E.920, E.921 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.919, A:E.920, A:E.921, A:E.921 GOL.17: 4 residues within 4Å: Chain A: G.735, K.737, D.745 Ligands: PEG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.735 GOL.18: 5 residues within 4Å: Chain A: H.612, H.708, K.711, T.729 Ligands: PEG.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.711 Water bridges: A:H.612, A:H.612 GOL.22: 8 residues within 4Å: Chain B: Y.511, R.566, L.897, I.900, S.901, I.905, E.906, Y.907 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.566, B:R.566 Water bridges: B:S.901 GOL.24: 7 residues within 4Å: Chain B: D.851, L.852, K.857, N.858, E.860, N.861, V.865 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.851 Water bridges: B:N.861, B:N.883 GOL.27: 9 residues within 4Å: Chain B: D.125, E.127, S.228, S.229, R.231, I.447, E.451, R.472, R.870 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.125, B:S.229, B:S.229, B:S.229, B:R.231, B:R.231 Water bridges: B:R.472, B:R.870 GOL.28: 6 residues within 4Å: Chain B: N.448, F.449, N.452, Y.453, I.516, Y.518 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.449, B:Y.453 GOL.29: 8 residues within 4Å: Chain B: E.124, D.125, Q.458, K.464, D.467, S.468, N.471, R.472 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.124, B:D.125, B:D.125, B:Q.458, B:N.471, B:R.472, B:R.472 Water bridges: B:D.467 GOL.30: 5 residues within 4Å: Chain B: K.775, L.779, R.844, I.845, F.848 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.775 GOL.32: 9 residues within 4Å: Chain B: N.713, K.734, N.743, I.744, D.745, Y.748, V.773, K.776, H.777 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.713, B:D.745, B:H.777 GOL.36: 6 residues within 4Å: Chain B: G.499, R.501, H.541, N.542, Y.553, D.624 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.501, B:H.541, B:N.542, B:Y.553 Water bridges: B:G.499, B:E.502, B:E.502, B:H.541 GOL.37: 4 residues within 4Å: Chain B: D.959, K.975, E.976, H.977 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.959, B:D.959, B:E.976 Water bridges: B:E.976

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

ACT.4: 5 residues within 4Å: Chain A: D.851, L.852, K.857, E.860, V.865 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.860 Water bridges: A:E.860 ACT.5: 5 residues within 4Å: Chain A: L.552, L.619, S.632, I.633, D.634 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.632, A:D.634 Water bridges: A:L.619 ACT.6: 4 residues within 4Å: Chain A: P.550, D.634, A.636, T.637 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.634 Salt bridges: A:K.640 ACT.7: 8 residues within 4Å: Chain A: E.124, D.125, Q.458, K.464, D.467, S.468, N.471, R.472 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.472 ACT.10: 5 residues within 4Å: Chain A: K.775, L.779, R.844, I.845, F.848 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.845, A:F.848 Water bridges: A:K.775 Salt bridges: A:K.775 ACT.12: 5 residues within 4Å: Chain A: W.710, T.763, E.765, Q.766, I.769 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.765 Hydrogen bonds: A:W.710, A:Q.766 ACT.21: 6 residues within 4Å: Chain A: Y.804, R.809 Chain B: A.293, E.296, D.297, Y.300 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.297 Hydrogen bonds: B:E.296 ACT.23: 4 residues within 4Å: Chain B: P.550, D.634, A.636, T.637 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.637 Hydrogen bonds: B:T.637 ACT.25: 7 residues within 4Å: Chain A: L.215, T.364, E.366, H.367 Chain B: T.364, E.366, H.367 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.364 Hydrogen bonds: B:T.364, A:T.364, A:E.366 Water bridges: A:H.367 Salt bridges: A:H.367 ACT.26: 7 residues within 4Å: Chain B: A.48, N.49, L.50, P.51, E.83, F.88, V.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.49, B:N.49 ACT.33: 6 residues within 4Å: Chain B: A.790, D.791, L.792, N.793, D.798, T.801 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.793 Hydrogen bonds: B:D.791, B:L.792

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

PEG.11: 9 residues within 4Å: Chain A: Q.306, D.323, Y.324, Y.325, P.326, E.327, K.330 Chain B: T.6, F.805 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.306, A:D.323, A:Y.325, A:E.327, A:K.330 Water bridges: A:Y.324, B:K.4 PEG.13: 7 residues within 4Å: Chain A: W.710, K.711, E.712, Y.730, G.735 Ligands: GOL.17, GOL.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.710 PEG.31: 9 residues within 4Å: Chain B: A.843, R.844, Y.847, I.917, L.918, R.919, E.920, E.921, F.946 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.918, B:R.919, B:E.920 Water bridges: B:D.851

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

CL.14: 8 residues within 4Å: Chain A: H.140, G.489, Q.490, T.491, Q.492, P.886, L.887, L.888 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain A: W.622, N.623, R.717, F.749, N.751, L.786 Ligand excluded by PLIP CL.34: 8 residues within 4Å: Chain B: H.140, G.489, Q.490, T.491, Q.492, P.886, L.887, L.888 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain B: W.622, N.623, R.717, F.749, N.751, L.786 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuga, T. et al., Effect of free cysteine residues to serine mutation on cellodextrin phosphorylase. To Be Published

Release Date

2024-12-25

Peptides

cellodextrin phosphorylase variant: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

cellodextrin phosphorylase variant

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