SMTL ID : 1kdg.1 (1 other biounit)

Crystal structure of the flavin domain of cellobiose dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.225 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 NAG.2: 6 residues within 4Å: Chain A: N.384, S.386, D.459, T.461, Q.462, A.470 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.384, A:S.386, A:S.386, A:T.461, A:Q.462 Water bridges: A:Q.462 NAG.3: 3 residues within 4Å: Chain A: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.318, A:N.390 NAG.13: 6 residues within 4Å: Chain B: N.384, S.386, D.459, T.461, Q.462, A.470 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.384, B:T.461, B:Q.462 Water bridges: B:Q.462 NAG.14: 3 residues within 4Å: Chain B: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.318, B:N.390

4 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.4: 3 residues within 4Å: Chain A: T.6, Y.8, K.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.32 MAN.15: 2 residues within 4Å: Chain B: T.2, V.3 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.2 MAN.16: 4 residues within 4Å: Chain B: S.4, A.5, T.6, P.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.4 MAN.17: 3 residues within 4Å: Chain B: T.6, Y.8, K.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.8, B:K.32

9 x HG: MERCURY (II) ION(Non-covalent)(Non-functional Binders)

HG.5: 2 residues within 4Å: Chain A: N.108, N.176 No protein-ligand interaction detected (PLIP) HG.6: 1 residues within 4Å: Chain B: F.79 No protein-ligand interaction detected (PLIP) HG.7: 2 residues within 4Å: Chain A: T.56, S.57 No protein-ligand interaction detected (PLIP) HG.8: 2 residues within 4Å: Ligands: HG.10, EMT.12 No protein-ligand interaction detected (PLIP) HG.9: 1 residues within 4Å: Ligands: EMT.12 No protein-ligand interaction detected (PLIP) HG.10: 1 residues within 4Å: Ligands: HG.8 No protein-ligand interaction detected (PLIP) HG.18: 2 residues within 4Å: Chain B: N.108, N.176 No protein-ligand interaction detected (PLIP) HG.19: 1 residues within 4Å: Chain A: F.79 No protein-ligand interaction detected (PLIP) HG.20: 2 residues within 4Å: Chain B: G.545, P.546 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.545, H2O.26

2 x 6FA: 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

6FA.11: 37 residues within 4Å: Chain A: V.13, G.14, A.15, G.16, P.17, G.18, E.37, R.38, F.69, F.73, W.81, G.90, C.91, L.92, G.95, G.96, T.97, V.99, N.100, G.101, A.102, L.103, V.217, M.218, V.219, S.256, A.257, G.258, I.265, N.479, H.480, D.512, A.513, N.523, P.524, Q.525, L.528 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.73, A:W.81, A:N.100, A:N.479 Hydrogen bonds: A:A.15, A:A.15, A:G.18, A:R.38, A:G.90, A:L.92, A:G.96, A:T.97, A:N.100, A:G.101, A:L.103, A:L.103, A:V.219, A:V.219, A:A.513, A:N.523, A:Q.525 Water bridges: A:G.16, A:R.38, A:A.259, A:A.259, A:G.261, A:R.264, A:N.479, A:N.479, A:W.481, A:G.526 pi-Cation interactions: A:R.38, A:H.480 6FA.21: 38 residues within 4Å: Chain B: V.13, G.14, A.15, G.16, P.17, G.18, E.37, R.38, F.69, F.73, W.81, F.88, G.90, C.91, L.92, G.95, G.96, T.97, V.99, N.100, G.101, A.102, L.103, V.217, M.218, V.219, S.256, A.257, G.258, I.265, N.479, H.480, D.512, A.513, N.523, P.524, Q.525, L.528 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:F.73, B:W.81, B:N.100, B:N.479 Hydrogen bonds: B:A.15, B:A.15, B:G.18, B:R.38, B:G.90, B:L.92, B:G.96, B:N.100, B:G.101, B:L.103, B:L.103, B:V.219, B:V.219, B:A.513, B:N.523, B:Q.525 Water bridges: B:G.16, B:R.38, B:A.259, B:A.259, B:G.261, B:R.264, B:N.479, B:W.481, B:G.526

1 x EMT: 2-(ETHYLMERCURI-THIO)-BENZOIC ACID(Non-covalent)

EMT.12: 8 residues within 4Å: Chain A: I.297, N.298, L.299, P.491, F.503, G.504 Ligands: HG.8, HG.9 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.297, A:L.299, A:P.491, A:P.491, A:F.503 Water bridges: A:N.298 Metal complexes: EMT.12

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.22: 4 residues within 4Å: Chain A: F.79, K.83 Chain B: F.79, K.83 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hallberg, B.M. et al., Crystal Structure of the Flavoprotein Domain of the Extracellular Flavocytochrome Cellobiose Dehydrogenase. J.Mol.Biol. (2002)

Release Date

2002-11-13

Peptides

cellobiose dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

cellobiose dehydrogenase

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