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Rubredoxin from desulfovibrio vulgaris miyazaki F, monoclinic crystal form

Analyse Rubredoxin from desulfovibrio vulgaris miyazaki F, monoclinic crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RDV
Type: protein
Length: 156 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.9
Source: Desulfovibrio vulgaris str. 'Miyazaki F'
Molecule: Rubredoxin
UniProt: P15412
Ligands: FE

Structure

x-ray diffraction · resolution 1.9 · 1 distinct chain · 17% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Rubredoxin	protein	52	17% helix, 23% strand	P15412

Ligands and binding sites

FE · Fe (III) ion · metal · 3 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

2 interfaces between chains.

A–C · 420 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 402 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2RDV · Rubredoxin from desulfovibrio vulgaris miyazaki F, monoclinic crystal form · the same entry in another collection · chain A against A, TM-score 1.00
P15412 · AlphaFold monomer V2.0 prediction for rubredoxin (P15412) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P15412
Elsewhere: RCSB PDB 2RDV · PDBe 2RDV · UniProt P15412

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