SMTL ID : 1d7d.1

CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, HP3 FRAGMENT, PH 7.5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: P.9, N.111, S.112, T.113, H.114 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 4 residues within 4Å: Chain B: P.9, V.49, N.111, H.114 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.49

6 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: P.21, D.24 Ligands: HEM.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.21, A:D.24, A:D.24, H2O.2, H2O.6 CD.4: 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.4, H2O.6, H2O.6, H2O.6 CD.5: 1 residues within 4Å: Chain A: E.126 No protein-ligand interaction detected (PLIP) CD.6: 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.2, H2O.7 CD.8: 3 residues within 4Å: Chain B: P.21, D.24 Ligands: HEM.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:P.21, B:D.24, B:D.24, H2O.7, H2O.7 CD.9: 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.7: 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.8 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 pi-Stacking: A:F.166 Metal complexes: A:H.163 HEM.10: 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.3 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 pi-Stacking: B:F.166 Metal complexes: B:H.163

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

1PG.11: 6 residues within 4Å: Chain A: Q.1, F.168, G.170 Chain B: Q.1, S.2, F.168 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.1, B:G.170, A:Q.1 Water bridges: A:G.170

Links

RCSB   PDBe   PDBe-KB   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)

Release Date

2000-10-18

Peptides

CELLOBIOSE DEHYDROGENASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CELLOBIOSE DEHYDROGENASE

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