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Crystal structure of thioredoxin L107A mutant

Analyse Crystal structure of thioredoxin L107A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HR1
Type: protein
Length: 715 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin-1
UniProt: P0AA27
Ligands: CU
Pockets: 7 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Thioredoxin-1	protein	107	36% helix, 26% strand	P0AA27
C, E, F	Thioredoxin-1	protein	106	34% helix, 27% strand	P0AA27
G	Thioredoxin-1	protein	76	36% helix, 17% strand	P0AA27

Ligands and binding sites

CU · Copper (II) ion · metal · 2 copies · chains A, B, D

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

Pockets

7 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	1042	0.82	0.83	103	empty
2	264	0.69	0.83	28	empty
3	88	0.45	0.80	17	empty
4	182	0.45	0.74	30	empty
5	98	0.43	0.78	16	empty

Interfaces

10 interfaces between chains.

A–B · 667 Å² buried · 16 hydrogen bonds · protein-protein
A–G · 428 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 288 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 246 Å² buried · 1 hydrogen bond · protein-protein
A–E · 229 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

5HR1 · Crystal structure of thioredoxin L107A mutant · the same entry in another collection · chain G against G, TM-score 1.00
P0AA27 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA27) · a predicted model of the same protein · chain C 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 P0AA27
Elsewhere: RCSB PDB 5HR1 · PDBe 5HR1 · UniProt P0AA27

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