MolNFT v1 · #83378 · protein

Crystal structure of ERP46 TRX1

3WGD · Thioredoxin domain-containing protein 5: “Crystal structure of ERP46 TRX1”. X-ray diffraction, 2 ligands (K, PO4), 6 pockets (best druggability 0.68). MolNFT v1 #83378 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WGD
Type: protein
Length: 995 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin domain-containing protein 5
UniProt: Q8NBS9
Ligands: K, PO4
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 5 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, I	Thioredoxin domain-containing protein 5	protein	111	41% helix, 21% strand	Q8NBS9
C	Thioredoxin domain-containing protein 5	protein	112	40% helix, 18% strand	Q8NBS9
F	Thioredoxin domain-containing protein 5	protein	109	41% helix, 18% strand	Q8NBS9
G	Thioredoxin domain-containing protein 5	protein	109	41% helix, 21% strand	Q8NBS9
H	Thioredoxin domain-containing protein 5	protein	110	41% helix, 20% strand	Q8NBS9

Ligands and binding sites

K · Potassium ion · metal · 5 copies · chains C, B, E, A, F, I
PO4 · Phosphate ion · ion · 15 copies · chains A, F, B, C, D, E, G, H, I
GOL · Glycerol · additive · 11 copies · chains A, B, F, C, E, G, H, I

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	444	0.68	0.80	54	empty
2	211	0.60	0.81	29	empty
3	148	0.49	0.78	28	empty
4	67	0.30	0.74	23	empty
5	54	0.29	0.75	11	PO4

Interfaces

9 interfaces between chains.

A–F · 522 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 521 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 515 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 499 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 494 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide (disulfide).

Compared structures

3WGD · Crystal structure of ERp46 Trx1 · the same entry in another collection · chain I against I, TM-score 1.00
Q8NBS9 · AlphaFold monomer V2.0 prediction for thioredoxin domain-containing protein 5 (Q8NBS9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q8NBS9
Elsewhere: RCSB PDB 3WGD · PDBe 3WGD · UniProt Q8NBS9

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