SMTL ID : 8xil.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

homo-dimer

Ligands

2 x BGC- BGC- BGC: beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-BGC-BGC.1: 17 residues within 4Å: Chain A: R.496, H.803, Y.804, R.809, E.810, F.815 Chain B: A.290, V.291, H.292, A.293, E.296, D.297, Y.300, E.328, F.329 Ligands: PEG.10, GOL.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.810, A:E.810 Water bridges: A:R.496, A:R.809, A:E.810 BGC-BGC-BGC.2: 17 residues within 4Å: Chain A: A.290, V.291, H.292, A.293, E.296, D.297, Y.300, E.328, F.329 Chain B: D.624, H.803, Y.804, R.809, E.810, F.815 Ligands: TRS.26, GOL.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.804, B:E.810, B:E.810 Water bridges: B:R.809

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

ACT.3: 6 residues within 4Å: Chain A: H.176, T.179, E.328, Q.331, D.332, K.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.179, A:D.332 Water bridges: A:D.332 Salt bridges: A:H.176 ACT.4: 4 residues within 4Å: Chain A: N.631, S.659, D.660, Y.661 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.631 ACT.6: 4 residues within 4Å: Chain A: A.679, E.680, T.683 Ligands: GOL.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.680 Hydrogen bonds: A:T.683 ACT.7: 6 residues within 4Å: Chain A: M.949, E.950, S.951, S.952, E.953, Y.954 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.952 ACT.8: 6 residues within 4Å: Chain A: T.362, G.363, A.369 Chain B: I.216, D.217, D.218 No protein-ligand interaction detected (PLIP) ACT.27: 10 residues within 4Å: Chain A: F.186, T.491, K.493, G.494 Chain B: A.293, I.294, F.295, E.296, D.297, V.298 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.186, A:K.493 Water bridges: A:K.493, B:D.297 Salt bridges: A:K.493 Hydrogen bonds: B:I.294, B:V.298 ACT.28: 2 residues within 4Å: Chain B: K.254, Y.432 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.432 ACT.30: 5 residues within 4Å: Chain B: Y.69, Q.72, F.73, I.98, P.101 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.69 Hydrogen bonds: B:Q.72

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

TRS.5: 10 residues within 4Å: Chain A: N.312, D.313, I.318, F.348, L.426, D.427, L.430, R.431, E.434 Chain B: I.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.312, A:D.313, A:D.427, A:D.427, A:R.431, A:E.434, A:E.434 TRS.26: 10 residues within 4Å: Chain B: W.622, N.623, D.624, S.625, L.786, E.810, F.815 Ligands: BGC-BGC-BGC.2, SO4.31, GOL.37 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.622, B:N.623, B:D.624, B:E.810 Water bridges: B:S.625, B:H.817 TRS.29: 11 residues within 4Å: Chain A: D.358, N.375, K.377 Chain B: D.33, A.34, V.35, A.54, P.55, V.56, M.57, Q.58 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.33, B:A.34, B:M.57, B:Q.58, B:Q.58, A:K.377 Water bridges: B:A.34, B:K.53, B:A.54, A:D.358, A:D.358, A:N.375

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 6 residues within 4Å: Chain A: R.486, H.817, Q.874, S.889, G.890, T.891 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.874, A:G.890 Water bridges: A:R.486, A:E.502, A:H.817, A:S.889 Salt bridges: A:R.486, A:H.817 SO4.31: 6 residues within 4Å: Chain B: R.486, H.817, Q.874, S.889, G.890 Ligands: TRS.26 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.486, B:R.486, B:Q.874, B:S.889, B:G.890 Water bridges: B:H.817, B:S.889 Salt bridges: B:H.817

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

PEG.10: 10 residues within 4Å: Chain A: R.501, H.541, N.542, Y.553, D.621, W.622, N.623, D.624 Ligands: BGC-BGC-BGC.1, GOL.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.501, A:R.501, A:H.541, A:D.624 Water bridges: A:D.624 PEG.11: 6 residues within 4Å: Chain A: L.17, K.21, K.42, N.43, S.78, E.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:K.42, A:E.93 PEG.12: 5 residues within 4Å: Chain A: S.951, S.952, E.953, K.984 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.953, A:K.984 PEG.32: 6 residues within 4Å: Chain A: V.291, H.292, F.295 Chain B: V.291, H.292, F.295 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.292, A:H.292 Water bridges: A:H.292 PEG.33: 5 residues within 4Å: Chain B: L.17, K.21, K.42, N.43, E.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.21, B:K.42, B:E.93

23 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 9 residues within 4Å: Chain A: R.155, A.531, N.532, N.540, F.543, W.545, V.546, G.547, A.584 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: N.713, K.734, I.744, D.745, Y.748, V.773, K.776, H.777 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: K.775, L.779, E.841, R.844, I.845, F.848 Ligand excluded by PLIP GOL.16: 9 residues within 4Å: Chain A: Y.456, Y.511, R.566, L.897, I.900, S.901, I.905, E.906, Y.907 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: R.341, N.342, G.343, T.399, V.400, I.401, S.436 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: G.256, N.414, V.421, R.424, E.425, N.428 Ligand excluded by PLIP GOL.19: 1 residues within 4Å: Chain A: D.835 Ligand excluded by PLIP GOL.20: 10 residues within 4Å: Chain A: P.943, V.944, G.945, F.946, A.947, S.952, F.983, K.984 Ligands: PEG.12, GOL.23 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain A: W.622, N.623, D.624, S.625, L.786, E.810, F.815 Ligands: BGC-BGC-BGC.1, PEG.10 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain A: A.679, T.683, A.691, Q.692, S.695 Ligands: ACT.6 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain A: N.836, E.837, K.840, F.946 Ligands: GOL.20 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain A: T.6, F.805 Chain B: Q.306, D.323, Y.324, Y.325, K.330 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain B: G.256, N.414, V.421, R.424, E.425, N.428 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain A: I.2 Chain B: N.312, I.318, F.348, D.427, L.430, R.431, E.434 Ligand excluded by PLIP GOL.37: 10 residues within 4Å: Chain B: R.501, H.541, Y.553, D.621, W.622, N.623, D.624 Ligands: BGC-BGC-BGC.2, TRS.26, GOL.45 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain B: V.233, T.245, T.247, R.265, E.267, E.440, L.443 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain B: R.341, N.342, G.343, T.399, V.400, I.401, S.436 Ligand excluded by PLIP GOL.40: 9 residues within 4Å: Chain B: F.459, F.466, Y.847, I.850, L.854, L.899, R.919, E.922, L.925 Ligand excluded by PLIP GOL.41: 6 residues within 4Å: Chain B: A.843, R.844, Y.847, R.919, E.920, E.921 Ligand excluded by PLIP GOL.42: 9 residues within 4Å: Chain B: E.528, A.531, N.532, N.540, F.543, W.545, V.546, G.547, A.584 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain B: Y.495, R.496, E.497, N.542, K.548, Q.549 Ligands: GOL.45 Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain B: N.631, S.659, D.660, Y.661 Ligand excluded by PLIP GOL.45: 7 residues within 4Å: Chain B: R.496, E.497, G.499, H.541, N.542 Ligands: GOL.37, GOL.43 Ligand excluded by PLIP

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

CL.24: 6 residues within 4Å: Chain A: W.622, N.623, R.717, F.749, N.751, L.786 Ligand excluded by PLIP CL.25: 7 residues within 4Å: Chain A: H.140, G.489, Q.490, T.491, Q.492, P.886, L.887 Ligand excluded by PLIP CL.46: 5 residues within 4Å: Chain B: P.51, S.113, D.114, V.115, K.116 Ligand excluded by PLIP CL.47: 6 residues within 4Å: Chain B: W.622, N.623, R.717, F.749, N.751, L.786 Ligand excluded by PLIP CL.48: 7 residues within 4Å: Chain B: H.140, G.489, Q.490, T.491, Q.492, P.886, L.887 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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cellodextrin phosphorylase

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