MolNFT v1 · #64843 · protein

L-threonine dehydrogenase (tktdh) from the hyperthermophilic archaeon thermococcus kodakaraensis

3GFB · L-threonine 3-dehydrogenase: “L-threonine dehydrogenase (tktdh) from the hyperthermophilic archaeon thermococcus kodakaraensis”. X-ray diffraction, 2 ligands (NAD, SO4), 14 pockets (best druggability 0.73). MolNFT v1 #64843 on…

PDB: 3GFB
Type: protein
Length: 1,388 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-threonine 3-dehydrogenase
EC: 1.1.1.103
UniProt: Q5JI69
Ligands: NAD, SO4
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	L-threonine 3-dehydrogenase (EC 1.1.1.103)	protein	347	31% helix, 28% strand	Q5JI69

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 10 copies · chains B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	713	0.73	0.79	60	NAD
2	696	0.72	0.78	59	NAD
3	712	0.69	0.76	64	NAD
4	667	0.69	0.77	57	NAD
5	219	0.68	0.85	51	empty

Interfaces

6 interfaces between chains.

A–B · 1670 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1641 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 706 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 688 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 619 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

3GFB · L-Threonine Dehydrogenase (TkTDH) from the hyperthermophilic archaeon Thermococcus… · the same entry in another collection · chain C against C, TM-score 1.00
Q5JI69 · AlphaFold monomer V2.0 prediction for L-threonine 3-dehydrogenase (Q5JI69) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q5JI69
Elsewhere: RCSB PDB 3GFB · PDBe 3GFB · UniProt Q5JI69

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