SMTL ID : 8j4x.3 (3 other biounits)

Structure of Mycobacterium tuberculosis NrdF2:NrdIcomplex (oxidised) determined at 3 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

hetero-2-1-mer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.72, E.103, H.106, F.167, I.193, E.197 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.72, A:H.106, A:E.197 MN.2: 4 residues within 4Å: Chain A: E.103, E.163, E.197, H.200 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.103, A:E.197, A:E.197, A:H.200 MN.5: 6 residues within 4Å: Chain B: D.72, E.103, H.106, I.193, E.197 Ligands: OH.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.72, B:E.103, B:H.106, B:E.197 MN.6: 5 residues within 4Å: Chain B: Q.75, E.103, E.163, E.197, H.200 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.103, B:E.197, B:E.197, B:H.200

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 6 residues within 4Å: Chain A: L.68, D.72, Y.110, F.167, F.171, I.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.110 OH.7: 7 residues within 4Å: Chain B: L.68, D.72, Y.110, F.167, F.171, I.193 Ligands: MN.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.110

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 2 residues within 4Å: Chain B: Y.146, E.233 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.146, B:E.233

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 21 residues within 4Å: Chain B: R.30, Y.202 Chain C: S.12, S.13, S.15, E.16, N.17, T.18, P.49, T.50, Y.51, G.52, Y.65, A.89, G.90, N.91, F.94, E.97, F.98, C.99, L.119 24 PLIP interactions: 3 interactions with chain B, 21 interactions with chain C Hydrophobic interactions: B:R.30, B:Y.202, C:Y.51, C:Y.51, C:F.94 Water bridges: B:N.269 Hydrogen bonds: C:S.13, C:E.16, C:N.17, C:N.17, C:T.18, C:T.18, C:T.50, C:T.50, C:Y.51, C:Y.51, C:G.52, C:N.91, C:E.97, C:C.99, C:L.119, C:L.119 pi-Stacking: C:F.94, C:F.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, L.R. et al., Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria. Curr Res Struct Biol (2024)

Release Date

2024-10-09

Peptides

Ribonucleoside-diphosphate reductase subunit beta nrdF2: AB
Protein NrdI: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
I

Ribonucleoside-diphosphate reductase subunit beta nrdF2

Protein NrdI

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