SMTL ID : 1d7d.1

CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, HP3 FRAGMENT, PH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x NAG: N-ACETYL-D-GLUCOSAMINE(Post Translational Modification)(Non-covalent)

NAG.1: 5 residues within 4Å: Chain A: N.111, S.112, T.113, H.114 Ligands: NAG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.113 Water bridges: A:N.111, A:N.111, A:T.113 NAG.2: 4 residues within 4Å: Chain A: P.9, H.114 Ligands: NAG.1, BMA.3 No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain B: V.49, N.111, H.114 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.111 Water bridges: B:N.111 NAG.10: 5 residues within 4Å: Chain B: P.9, V.49, H.114 Ligands: NAG.9, MAN.11 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.49

1 x BMA: BETA-D-MANNOSE(Non-covalent)

BMA.3: 2 residues within 4Å: Chain A: P.9 Ligands: NAG.2 No protein-ligand interaction detected (PLIP)

6 x CD: CADMIUM ION(Non-covalent)

CD.4: 3 residues within 4Å: Chain A: P.21, D.24 Ligands: HEM.14 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.21, A:D.24, A:D.24, H2O.2713, H2O.2713 CD.5: 3 residues within 4Å: Chain A: E.107, Y.184, N.186 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.107, H2O.2714, H2O.2714, H2O.2714, H2O.2714 CD.6: 1 residues within 4Å: Chain A: E.126 No protein-ligand interaction detected (PLIP) CD.7: 2 residues within 4Å: Chain A: D.165 Chain B: D.165 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.165, B:D.165, B:D.165, H2O.2716, H2O.2716 CD.12: 3 residues within 4Å: Chain B: P.21, D.24 Ligands: HEM.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.21, B:D.24, B:D.24, H2O.2799, H2O.2799 CD.13: 3 residues within 4Å: Chain B: E.107, Y.184, N.186 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.107

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.8: 21 residues within 4Å: Chain A: W.56, G.58, I.59, A.64, M.65, L.70, L.71, V.72, Y.90, Q.92, P.93, A.142, A.144, F.160, E.162, H.163, F.166, F.168 Chain B: P.21, D.24 Ligands: CD.12 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.56, A:M.65, A:L.70, A:Y.90, A:Y.90, A:A.142, A:A.144, A:E.162, A:E.162, A:F.166, A:F.166, A:F.168 Hydrogen bonds: A:M.65 Water bridges: A:N.66 Metal complexes: A:H.163 pi-Stacking: A:F.166 HEM.14: 21 residues within 4Å: Chain A: P.21, D.24 Chain B: W.56, G.58, I.59, A.64, M.65, L.70, L.71, V.72, Y.90, Q.92, P.93, A.142, A.144, F.160, E.162, H.163, F.166, F.168 Ligands: CD.4 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:W.56, B:W.56, B:M.65, B:L.70, B:Y.90, B:Q.92, B:A.142, B:A.144, B:E.162, B:E.162, B:F.166, B:F.166, B:F.168 Hydrogen bonds: B:M.65, B:Y.90 Water bridges: B:N.66 Metal complexes: B:H.163 pi-Stacking: B:F.166

1 x MAN: ALPHA-D-MANNOSE(Non-covalent)

MAN.11: 2 residues within 4Å: Chain B: P.9 Ligands: NAG.10 No protein-ligand interaction detected (PLIP)

1 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.15: 6 residues within 4Å: Chain A: E.1, F.168, G.170 Chain B: E.1, S.2, F.168 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.1, B:E.1, B:G.170

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hallberg, B.M. et al., A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase. Structure Fold.Des. (2000)

Peptides

CELLOBIOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CELLOBIOSE DEHYDROGENASE

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