SMTL ID : 8j4w.1

Structure of Mycobacterium thermoresistibile NrdI(reduced) determined at 1.1 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

monomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: S.10, S.11, S.13, E.14, Y.15, T.16, P.47, T.48, Y.49, G.50, G.51, Y.63, A.87, G.88, N.89, F.92, E.95, F.96, A.97, L.117 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.11, A:S.13, A:Y.15, A:T.16, A:T.16, A:T.48, A:T.48, A:N.89, A:E.95, A:A.97, A:L.117, A:L.117 pi-Stacking: A:F.92, A:F.92

1 x SO3: SULFITE ION(Non-covalent)

SO3.2: 6 residues within 4Å: Chain A: F.9, S.11, L.32, Y.49, K.66, Q.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.67 Water bridges: A:K.66, A:K.66

1 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.3: 5 residues within 4Å: Chain A: V.3, G.4, L.131, A.132, W.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.4 Water bridges: A:A.132, A:A.132

1 x PER: PEROXIDE ION(Non-covalent)

PER.4: 3 residues within 4Å: Chain A: L.72, R.78, C.107 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: V.12 Ligand excluded by PLIP

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

Protein NrdI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Protein NrdI

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