MolNFT v1 · #73600 · protein

Mycobacterium tuberculosis thioredoxin C C40S mutant in complex with quinol inhibitor PMX464

3O6T: “Mycobacterium tuberculosis thioredoxin C C40S mutant in complex with quinol inhibitor PMX464”. X-ray diffraction, 1 ligand (PX5), 3 pockets (best druggability 0.78). MolNFT v1 #73600 on GenesisL1: 3D structure, binding sites and…

PDB: 3O6T
Type: protein
Length: 435 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thioredoxin
UniProt: P0A616
Ligands: PX5
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Thioredoxin	protein	108	28% helix, 24% strand	P0A616
B	Thioredoxin	protein	110	33% helix, 25% strand	P0A616
D	Thioredoxin	protein	109	31% helix, 25% strand	P0A616

Ligands and binding sites

PX5 · 4-(1,3-benzothiazol-2-yl)-4-hydroxycyclohexa-2,5-dien-1-one · ligand · 2 copies · chains A, B, C, D
PGE · Triethylene glycol · additive · 2 copies · chains A, D, B, C

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

Pockets

3 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	622	0.78	0.84	67	empty
2	434	0.62	0.76	42	empty
3	114	0.45	0.78	17	empty

Interfaces

6 interfaces between chains.

B–C · 566 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 561 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 446 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 419 Å² buried · 1 hydrogen bond · protein-protein
B–D · 75 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

3O6T · Mycobacterium tuberculosis thioredoxin C C40S mutant in Complex with Quinol Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00

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 P0A616
Elsewhere: RCSB PDB 3O6T · PDBe 3O6T · UniProt P0A616

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