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NMR and X-ray analysis of structural additivity in metal binding site- swapped hybrids of rubredoxin

Analyse NMR and X-ray analysis of structural additivity in metal binding site- swapped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PVE
Type: protein
Length: 156 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rubredoxin
UniProt: P00268
Ligands: ZN
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 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	P00268

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B, C
ACT · Acetate ion · additive · 3 copies · chains A, C
EDO · 1,2-ethanediol · additive · chains B, C

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.30	0.76	18	empty

Interfaces

3 interfaces between chains.

A–C · 368 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 352 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 25 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2PVE · NMR and X-ray Analysis of Structural Additivity in Metal Binding Site-Swapped Hybrids of… · the same entry in another collection · chain A against A, TM-score 1.00
P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P00268
Elsewhere: RCSB PDB 2PVE · PDBe 2PVE · UniProt P00268

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