MolNFT v1 · #139931 · protein

Crystal structure of RV2466C C22S mutant

5XUR · Thioredoxin-like reductase RV2466C: “Crystal structure of RV2466C C22S mutant”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.78). MolNFT v1 #139931 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XUR
Type: protein
Length: 789 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin-like reductase RV2466C
UniProt: O53193
Ligands: CL
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thioredoxin-like reductase RV2466C	protein	200	50% helix, 18% strand	O53193
B	Thioredoxin-like reductase RV2466C	protein	195	50% helix, 18% strand	O53193
C	Thioredoxin-like reductase RV2466C	protein	193	52% helix, 18% strand	O53193
D	Thioredoxin-like reductase RV2466C	protein	201	49% helix, 17% strand	O53193

Ligands and binding sites

CL · Chloride ion · ion · chains B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, D

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1039	0.78	0.80	94	EDO
2	548	0.76	0.83	60	empty
3	525	0.76	0.83	55	empty
4	133	0.52	0.81	25	empty
5	105	0.38	0.75	17	empty

Interfaces

6 interfaces between chains.

A–B · 2334 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2146 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 1038 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 916 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 820 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5XUR · Crystal Structure of Rv2466c C22S Mutant · the same entry in another collection · chain D against D, TM-score 1.00
O53193 · AlphaFold monomer V2.0 prediction for thioredoxin-like reductase RV2466C (O53193) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 O53193
Elsewhere: RCSB PDB 5XUR · PDBe 5XUR · UniProt O53193

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