SMTL ID : 4eib.1

Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight into the Altered Selectivity on Carbohydrate Binding.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.66, W.67, N.68, N.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.67, A:N.68, A:N.69, A:N.69 SO4.2: 2 residues within 4Å: Chain A: A.27, S.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.28 Water bridges: A:S.26 SO4.4: 2 residues within 4Å: Chain A: K.48, N.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.86 Salt bridges: A:K.48 SO4.16: 4 residues within 4Å: Chain B: N.66, W.67, N.68, N.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.66, B:W.67, B:N.68, B:N.69, B:N.69 SO4.17: 2 residues within 4Å: Chain B: A.27, S.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.28 Water bridges: B:V.29 SO4.18: 2 residues within 4Å: Chain B: K.48, N.86 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86 Salt bridges: B:K.48

4 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 5 residues within 4Å: Chain A: I.74, A.75 Chain B: I.74, A.75 Ligands: NA.23 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.75, A:A.75, A:A.75 NH4.19: 3 residues within 4Å: Chain B: Y.6, N.8 Ligands: CL.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.8 NH4.32: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.33: 3 residues within 4Å: Chain B: Y.6, D.7, N.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.8, B:N.8

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

NA.5: 1 residues within 4Å: Chain A: A.12 No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain A: A.12, N.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 NA.7: 3 residues within 4Å: Chain A: Y.6, D.7, N.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.7, A:D.7, A:N.8 Water bridges: A:S.11 NA.8: 3 residues within 4Å: Chain A: D.62, G.63, G.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.63 Water bridges: A:K.97 NA.9: 2 residues within 4Å: Chain A: Y.103, K.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.103 NA.10: 2 residues within 4Å: Chain A: S.33, Y.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.34, A:Y.34 NA.20: 3 residues within 4Å: Chain B: P.81, I.82, S.83 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.83, B:S.83 NA.21: 2 residues within 4Å: Chain B: S.33, Y.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.34, B:Y.34 NA.22: 2 residues within 4Å: Chain B: A.27, Q.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.30 Water bridges: B:V.29 NA.23: 4 residues within 4Å: Chain B: A.75, F.92, S.93 Ligands: NH4.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.75, B:S.93 NA.24: 5 residues within 4Å: Chain B: K.55, V.56, T.57, K.105, E.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.57, B:K.105 NA.25: 2 residues within 4Å: Chain B: E.101 Ligands: CL.31 No protein-ligand interaction detected (PLIP)

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

CL.11: 3 residues within 4Å: Chain A: D.7, N.9, Y.14 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: S.33, Y.34, G.43 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: T.40, S.93, A.94 Chain B: S.77 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: N.49, A.51, Y.52 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain B: N.8, N.13 Ligands: NH4.19 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain B: G.63, K.97, G.98 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: S.33, Y.34, N.35, G.43 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: A.12 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: N.49, S.85, N.86 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain B: D.65, W.67, E.101 Ligands: NA.25 Ligand excluded by PLIP

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

ACT.15: 3 residues within 4Å: Chain A: N.9, Y.14, Q.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.15 Hydrogen bonds: A:N.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stephen, P. et al., Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites. Plos One (2012)

Release Date

2012-12-12

Peptides

Glucoamylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucoamylase