SMTL ID : 6icl.1

Pseudomonas putida CBB5 NdmB

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 10 residues within 4Å: Chain A: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.82, A:H.84, A:C.105, A:H.108 FES.3: 10 residues within 4Å: Chain B: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.82, B:H.84, B:C.105, B:H.108 FES.5: 10 residues within 4Å: Chain C: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.82, C:H.84, C:C.105, C:H.108 FES.7: 10 residues within 4Å: Chain D: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.82, D:H.84, D:C.105, D:H.108 FES.9: 10 residues within 4Å: Chain E: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.82, E:H.84, E:C.105, E:H.108 FES.11: 10 residues within 4Å: Chain F: C.82, H.84, R.85, S.86, A.87, C.105, Y.107, H.108, G.109, W.110 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.82, F:H.84, F:C.105, F:H.108

6 x FE: FE (III) ION(Non-covalent)

FE.2: 4 residues within 4Å: Chain A: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.197, A:H.202, A:D.314, A:D.314, H2O.6 FE.4: 4 residues within 4Å: Chain B: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.197, B:H.202, B:D.314, B:D.314, H2O.12 FE.6: 4 residues within 4Å: Chain C: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.197, C:H.202, C:D.314, C:D.314, H2O.18 FE.8: 4 residues within 4Å: Chain D: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.197, D:H.202, D:D.314, D:D.314, H2O.24 FE.10: 4 residues within 4Å: Chain E: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.197, E:H.202, E:D.314, E:D.314, H2O.30 FE.12: 4 residues within 4Å: Chain F: N.191, H.197, H.202, D.314 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.197, F:H.202, F:D.314, F:D.314, H2O.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, J.H. et al., Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. J.Mol.Biol. (2019)

Release Date

2019-09-04

Peptides

Methylxanthine N3-demethylase NdmB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Methylxanthine N3-demethylase NdmB