SMTL ID : 4qi3.3 (2 other biounits)

Cytochrome domain of Myriococcum thermophilum cellobiose dehydrogenase, MtCYT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 24 residues within 4Å: Chain A: W.65, G.67, I.68, G.72, P.73, M.74, L.79, I.80, T.81, Y.99, M.101, P.102, G.154, W.155, V.156, L.173, Q.174, Q.175, H.176, M.180, I.182 Chain B: V.150, Q.186 Ligands: MG.8 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:W.65, A:L.79, A:L.79, A:Y.99, A:M.101, A:P.102, A:V.156, A:L.173, A:L.173, A:Q.175, A:Q.175, A:I.182 Hydrogen bonds: A:M.74, A:Y.99, B:Q.186 Metal complexes: A:H.176 HEM.9: 24 residues within 4Å: Chain A: V.150, Q.186 Chain B: W.65, G.67, I.68, G.72, P.73, M.74, L.79, I.80, T.81, Y.99, M.101, P.102, G.154, W.155, V.156, L.173, Q.174, Q.175, H.176, M.180, I.182 Ligands: MG.7 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:W.65, B:L.79, B:L.79, B:Y.99, B:M.101, B:P.102, B:V.156, B:L.173, B:L.173, B:Q.175, B:Q.175, B:I.182 Hydrogen bonds: B:M.74, B:Y.99, A:Q.186 Water bridges: B:Q.175 Metal complexes: B:H.176

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

NAG.2: 5 residues within 4Å: Chain A: K.56, S.117, N.119, H.122, S.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.119, A:S.124, A:S.124 NAG.10: 5 residues within 4Å: Chain B: K.56, S.117, N.119, T.121, H.122 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.117, B:N.119, B:T.121, B:T.121, B:S.124, B:S.124

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

MAN.3: 3 residues within 4Å: Chain A: S.193, S.195, W.199 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.13, A:G.14, A:W.199 MAN.4: 3 residues within 4Å: Chain A: P.194, T.197, D.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.194, A:D.198 MAN.5: 1 residues within 4Å: Chain A: T.204 No protein-ligand interaction detected (PLIP) MAN.6: 4 residues within 4Å: Chain A: E.110, T.112, T.204, T.206 No protein-ligand interaction detected (PLIP) MAN.11: 3 residues within 4Å: Chain B: S.195, D.198, W.199 No protein-ligand interaction detected (PLIP) MAN.12: 2 residues within 4Å: Chain B: T.197, D.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.198 MAN.13: 3 residues within 4Å: Chain B: V.114, T.204, K.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.114 MAN.14: 5 residues within 4Å: Chain B: E.110, T.112, A.203, T.204, T.206 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.204

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: G.149, Q.186 Ligands: HEM.9 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.149, H2O.1, H2O.7, H2O.7 MG.8: 3 residues within 4Å: Chain B: G.149, Q.186 Ligands: HEM.1 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:G.149, H2O.1, H2O.1, H2O.7 MG.15: 1 residues within 4Å: Chain B: D.108 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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