SMTL ID : 1kdg.2 (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-hexamer

Ligands

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

NAG.1: 6 residues within 4Å: Chain A: N.225 Chain E: M.303, N.304, R.408, G.409, R.410 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:N.225, E:N.304, E:N.304, E:G.409 Water bridges: E:T.423 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: 7 residues within 4Å: Chain B: N.384, S.386, D.459, T.461, Q.462, A.470 Chain D: P.388 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 NAG.23: 6 residues within 4Å: Chain A: M.303, N.304, R.408, G.409, R.410 Chain C: N.225 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.304, A:N.304, A:G.409, C:N.225 Water bridges: A:T.423 NAG.24: 6 residues within 4Å: Chain C: N.384, S.386, D.459, T.461, Q.462, A.470 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.384, C:S.386, C:S.386, C:T.461, C:Q.462 Water bridges: C:Q.462 NAG.25: 3 residues within 4Å: Chain C: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.318, C:N.390 NAG.35: 7 residues within 4Å: Chain D: N.384, S.386, D.459, T.461, Q.462, A.470 Chain F: P.388 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.384, D:T.461, D:Q.462 Water bridges: D:Q.462 NAG.36: 3 residues within 4Å: Chain D: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.318, D:N.390 NAG.45: 6 residues within 4Å: Chain C: M.303, N.304, R.408, G.409, R.410 Chain E: N.225 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:N.304, C:N.304, C:G.409, E:N.225 Water bridges: C:T.423 NAG.46: 6 residues within 4Å: Chain E: N.384, S.386, D.459, T.461, Q.462, A.470 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.384, E:S.386, E:S.386, E:T.461, E:Q.462 Water bridges: E:Q.462 NAG.47: 3 residues within 4Å: Chain E: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:P.318, E:N.390 NAG.57: 7 residues within 4Å: Chain B: P.388 Chain F: N.384, S.386, D.459, T.461, Q.462, A.470 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.384, F:T.461, F:Q.462 Water bridges: F:Q.462 NAG.58: 3 residues within 4Å: Chain F: P.318, N.390, Q.393 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:P.318, F:N.390

12 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 MAN.26: 3 residues within 4Å: Chain C: T.6, Y.8, K.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.32 MAN.37: 2 residues within 4Å: Chain D: T.2, V.3 1 PLIP interactions: 1 interactions with chain D Water bridges: D:T.2 MAN.38: 4 residues within 4Å: Chain D: S.4, A.5, T.6, P.7 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.4 MAN.39: 3 residues within 4Å: Chain D: T.6, Y.8, K.32 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.8, D:K.32 MAN.48: 3 residues within 4Å: Chain E: T.6, Y.8, K.32 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.32 MAN.59: 2 residues within 4Å: Chain F: T.2, V.3 1 PLIP interactions: 1 interactions with chain F Water bridges: F:T.2 MAN.60: 4 residues within 4Å: Chain F: S.4, A.5, T.6, P.7 1 PLIP interactions: 1 interactions with chain F Water bridges: F:S.4 MAN.61: 3 residues within 4Å: Chain F: T.6, Y.8, K.32 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.8, F:K.32

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

HG.5: 2 residues within 4Å: Chain A: N.108, N.176 Ligand excluded by PLIP HG.6: 1 residues within 4Å: Chain B: F.79 Ligand excluded by PLIP HG.7: 2 residues within 4Å: Chain A: T.56, S.57 Ligand excluded by PLIP HG.8: 7 residues within 4Å: Ligands: HG.10, EMT.12, HG.30, HG.32, EMT.34, HG.52, EMT.56 Ligand excluded by PLIP HG.9: 5 residues within 4Å: Ligands: EMT.12, HG.31, EMT.34, HG.53, EMT.56 Ligand excluded by PLIP HG.10: 2 residues within 4Å: Ligands: HG.8, HG.52 Ligand excluded by PLIP HG.18: 2 residues within 4Å: Chain B: N.108, N.176 Ligand excluded by PLIP HG.19: 1 residues within 4Å: Chain A: F.79 Ligand excluded by PLIP HG.20: 2 residues within 4Å: Chain B: G.545, P.546 Ligand excluded by PLIP HG.27: 2 residues within 4Å: Chain C: N.108, N.176 Ligand excluded by PLIP HG.28: 1 residues within 4Å: Chain D: F.79 Ligand excluded by PLIP HG.29: 2 residues within 4Å: Chain C: T.56, S.57 Ligand excluded by PLIP HG.30: 7 residues within 4Å: Ligands: HG.8, EMT.12, HG.32, EMT.34, HG.52, HG.54, EMT.56 Ligand excluded by PLIP HG.31: 5 residues within 4Å: Ligands: HG.9, EMT.12, EMT.34, HG.53, EMT.56 Ligand excluded by PLIP HG.32: 2 residues within 4Å: Ligands: HG.8, HG.30 Ligand excluded by PLIP HG.40: 2 residues within 4Å: Chain D: N.108, N.176 Ligand excluded by PLIP HG.41: 1 residues within 4Å: Chain C: F.79 Ligand excluded by PLIP HG.42: 2 residues within 4Å: Chain D: G.545, P.546 Ligand excluded by PLIP HG.49: 2 residues within 4Å: Chain E: N.108, N.176 Ligand excluded by PLIP HG.50: 1 residues within 4Å: Chain F: F.79 Ligand excluded by PLIP HG.51: 2 residues within 4Å: Chain E: T.56, S.57 Ligand excluded by PLIP HG.52: 7 residues within 4Å: Ligands: HG.8, HG.10, EMT.12, HG.30, EMT.34, HG.54, EMT.56 Ligand excluded by PLIP HG.53: 5 residues within 4Å: Ligands: HG.9, EMT.12, HG.31, EMT.34, EMT.56 Ligand excluded by PLIP HG.54: 2 residues within 4Å: Ligands: HG.30, HG.52 Ligand excluded by PLIP HG.62: 2 residues within 4Å: Chain F: N.108, N.176 Ligand excluded by PLIP HG.63: 1 residues within 4Å: Chain E: F.79 Ligand excluded by PLIP HG.64: 2 residues within 4Å: Chain F: G.545, P.546 Ligand excluded by PLIP

6 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 6FA.33: 37 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:F.73, C:W.81, C:N.100, C:N.479 Hydrogen bonds: C:A.15, C:A.15, C:G.18, C:R.38, C:G.90, C:L.92, C:G.96, C:T.97, C:N.100, C:G.101, C:L.103, C:L.103, C:V.219, C:V.219, C:A.513, C:N.523, C:Q.525 Water bridges: C:G.16, C:R.38, C:A.259, C:A.259, C:G.261, C:R.264, C:N.479, C:N.479, C:W.481, C:G.526 pi-Cation interactions: C:R.38, C:H.480 6FA.43: 38 residues within 4Å: Chain D: 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 D Hydrophobic interactions: D:F.73, D:W.81, D:N.100, D:N.479 Hydrogen bonds: D:A.15, D:A.15, D:G.18, D:R.38, D:G.90, D:L.92, D:G.96, D:N.100, D:G.101, D:L.103, D:L.103, D:V.219, D:V.219, D:A.513, D:N.523, D:Q.525 Water bridges: D:G.16, D:R.38, D:A.259, D:A.259, D:G.261, D:R.264, D:N.479, D:W.481, D:G.526 6FA.55: 37 residues within 4Å: Chain E: 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 E Hydrophobic interactions: E:F.73, E:W.81, E:N.100, E:N.479 Hydrogen bonds: E:A.15, E:A.15, E:G.18, E:R.38, E:G.90, E:L.92, E:G.96, E:T.97, E:N.100, E:G.101, E:L.103, E:L.103, E:V.219, E:V.219, E:A.513, E:N.523, E:Q.525 Water bridges: E:G.16, E:R.38, E:A.259, E:A.259, E:G.261, E:R.264, E:N.479, E:N.479, E:W.481, E:G.526 pi-Cation interactions: E:R.38, E:H.480 6FA.65: 38 residues within 4Å: Chain F: 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 F Hydrophobic interactions: F:F.73, F:W.81, F:N.100, F:N.479 Hydrogen bonds: F:A.15, F:A.15, F:G.18, F:R.38, F:G.90, F:L.92, F:G.96, F:N.100, F:G.101, F:L.103, F:L.103, F:V.219, F:V.219, F:A.513, F:N.523, F:Q.525 Water bridges: F:G.16, F:R.38, F:A.259, F:A.259, F:G.261, F:R.264, F:N.479, F:W.481, F:G.526

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

EMT.12: 14 residues within 4Å: Chain A: I.297, N.298, L.299, P.491, F.503, G.504 Ligands: HG.8, HG.9, HG.30, HG.31, EMT.34, HG.52, HG.53, EMT.56 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 EMT.34: 14 residues within 4Å: Chain C: I.297, N.298, L.299, P.491, F.503, G.504 Ligands: HG.8, HG.9, EMT.12, HG.30, HG.31, HG.52, HG.53, EMT.56 7 PLIP interactions: 6 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:I.297, C:L.299, C:P.491, C:P.491, C:F.503 Water bridges: C:N.298 Metal complexes: EMT.34 EMT.56: 14 residues within 4Å: Chain E: I.297, N.298, L.299, P.491, F.503, G.504 Ligands: HG.8, HG.9, EMT.12, HG.30, HG.31, EMT.34, HG.52, HG.53 7 PLIP interactions: 6 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:I.297, E:L.299, E:P.491, E:P.491, E:F.503 Water bridges: E:N.298 Metal complexes: EMT.56

3 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) UNX.44: 4 residues within 4Å: Chain C: F.79, K.83 Chain D: F.79, K.83 No protein-ligand interaction detected (PLIP) UNX.66: 4 residues within 4Å: Chain E: F.79, K.83 Chain F: 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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

cellobiose dehydrogenase

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