SMTL ID : 4qi7.3 (2 other biounits)

Cellobiose dehydrogenase from Neurospora crassa, NcCDH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 20 residues within 4Å: Chain A: W.65, G.67, V.68, A.73, M.74, L.79, I.80, Y.99, M.101, P.102, G.154, W.155, V.156, L.173, S.174, Q.175, H.176, M.180, G.181, Q.182 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.65, A:W.65, A:M.74, A:L.79, A:L.79, A:L.79, A:Y.99, A:Y.99, A:Y.99, A:M.101, A:P.102, A:V.156, A:Q.175, A:Q.175 Hydrogen bonds: A:M.74, A:Y.99 Metal complexes: A:H.176 HEM.27: 21 residues within 4Å: Chain B: W.65, G.67, V.68, A.73, M.74, L.79, I.80, T.81, Y.99, M.101, P.102, G.154, W.155, V.156, L.173, S.174, Q.175, H.176, M.180, G.181, Q.182 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.65, B:W.65, B:M.74, B:L.79, B:L.79, B:L.79, B:Y.99, B:Y.99, B:M.101, B:P.102, B:V.156, B:V.156, B:Q.175, B:Q.175 Hydrogen bonds: B:M.74, B:Y.99 Metal complexes: B:H.176

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 34 residues within 4Å: Chain A: V.235, G.236, G.237, G.238, A.239, G.240, E.259, K.260, W.295, M.309, G.311, C.312, V.313, G.316, G.317, N.321, A.322, L.324, T.438, A.439, V.440, S.479, A.480, G.481, I.488, N.699, H.700, D.736, A.737, N.747, P.748, T.749, I.752 Ligands: MG.24 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:W.295, A:N.321, A:N.699 Hydrogen bonds: A:G.237, A:A.239, A:G.240, A:K.260, A:G.311, A:G.316, A:G.317, A:G.317, A:N.321, A:A.322, A:L.324, A:L.324, A:V.440, A:V.440, A:A.737, A:N.747, A:T.749, A:T.749, A:T.749 pi-Stacking: A:H.700, A:H.700 FAD.28: 32 residues within 4Å: Chain B: V.235, G.236, G.238, A.239, G.240, I.258, E.259, K.260, W.295, M.309, G.311, C.312, V.313, G.316, G.317, N.321, A.322, L.324, T.438, A.439, V.440, S.479, A.480, G.481, I.488, N.699, D.736, A.737, N.747, P.748, T.749, I.752 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:W.295, B:N.699 Hydrogen bonds: B:G.237, B:A.239, B:G.240, B:K.260, B:G.311, B:V.313, B:G.317, B:N.321, B:A.322, B:V.440, B:V.440, B:A.737, B:N.747, B:T.749, B:T.749, B:T.749 pi-Cation interactions: B:H.700

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

NAG.3: 4 residues within 4Å: Chain A: N.119, T.121, H.122, T.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.121, A:T.121, A:T.124, A:T.124 NAG.4: 4 residues within 4Å: Chain A: E.275, N.278 Chain B: G.461 Ligands: MAN.35 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: N.400, R.401, E.584 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.400 NAG.6: 3 residues within 4Å: Chain A: N.471, T.472, A.791 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.791 NAG.7: 3 residues within 4Å: Chain A: K.497, K.504, N.515 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.497, A:K.504, A:N.515 NAG.8: 4 residues within 4Å: Chain A: Q.373, H.539, N.541, K.669 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.669 NAG.9: 3 residues within 4Å: Chain A: N.555, T.557, D.558 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.555 NAG.29: 3 residues within 4Å: Chain B: N.119, H.122, T.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.119, B:T.124, B:T.124 NAG.30: 4 residues within 4Å: Chain A: G.461 Chain B: E.275, N.278 Ligands: MAN.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.278 NAG.31: 5 residues within 4Å: Chain B: N.400, R.401, E.584, T.586, V.592 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.592 Hydrogen bonds: B:N.400, B:E.584 NAG.32: 3 residues within 4Å: Chain B: K.497, K.504, N.515 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.497, B:K.504, B:N.515 NAG.33: 3 residues within 4Å: Chain B: V.377, N.380, N.541 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.380 NAG.34: 2 residues within 4Å: Chain B: N.555, T.557 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.555

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

MAN.10: 5 residues within 4Å: Chain A: A.220, T.222, G.461 Chain B: E.275 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) MAN.11: 1 residues within 4Å: Chain A: T.226 No protein-ligand interaction detected (PLIP) MAN.35: 5 residues within 4Å: Chain B: T.222, N.460, G.461, Y.463 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.460, B:Y.463 MAN.36: 1 residues within 4Å: Chain B: T.226 No protein-ligand interaction detected (PLIP)

20 x PT: PLATINUM (II) ION(Non-functional Binders)(Non-covalent)

PT.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.14: 1 residues within 4Å: Chain A: D.647 Ligand excluded by PLIP PT.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.16: 2 residues within 4Å: Chain A: K.331, Y.335 Ligand excluded by PLIP PT.17: 1 residues within 4Å: Chain A: K.273 Ligand excluded by PLIP PT.18: 1 residues within 4Å: Chain A: R.697 Ligand excluded by PLIP PT.19: 1 residues within 4Å: Chain A: K.433 Ligand excluded by PLIP PT.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.23: 1 residues within 4Å: Chain B: A.100 Ligand excluded by PLIP PT.37: 1 residues within 4Å: Chain B: P.781 Ligand excluded by PLIP PT.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PT.40: 2 residues within 4Å: Chain B: K.331, Y.335 Ligand excluded by PLIP PT.41: 1 residues within 4Å: Chain B: K.273 Ligand excluded by PLIP PT.42: 1 residues within 4Å: Chain B: R.697 Ligand excluded by PLIP PT.43: 1 residues within 4Å: Chain B: K.433 Ligand excluded by PLIP PT.44: 1 residues within 4Å: Chain B: S.351 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.24: 2 residues within 4Å: Chain A: L.324 Ligands: FAD.2 No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain A: D.177, M.180 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.177 MG.45: 3 residues within 4Å: Chain B: S.632, T.634, N.636 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, T.C. et al., Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat Commun (2015)

Release Date

2015-07-15

Peptides

Cellobiose dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cellobiose dehydrogenase

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