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mouse TDH with NAD+ bound

Analyse mouse TDH with NAD+ bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YR9
Type: protein
Length: 1,839 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.8
Source: Mus musculus
Molecule: L-threonine 3-dehydrogenase, mitochondrial
EC: 1.1.1.103
UniProt: Q8K3F7
Ligands: NAD
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.8 · 4 distinct chains · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E	L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103)	protein	308	46% helix, 17% strand	Q8K3F7
B	L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103)	protein	307	46% helix, 17% strand	Q8K3F7
C	L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103)	protein	307	43% helix, 17% strand	Q8K3F7
F	L-threonine 3-dehydrogenase, mitochondrial (EC 1.1.1.103)	protein	301	41% helix, 17% strand	Q8K3F7

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	632	0.77	0.82	60	NAD, GOL
2	513	0.77	0.84	60	NAD
3	444	0.76	0.85	48	NAD, GOL
4	588	0.76	0.83	62	NAD
5	511	0.76	0.84	46	NAD

Interfaces

7 interfaces between chains.

B–D · 1501 Å² buried · 30 hydrogen bonds · protein-protein
E–F · 1493 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1491 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 620 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 555 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4YR9 · Mouse tdh with NAD+ bound · the same entry in another collection · chain F against F, TM-score 1.00
Q8K3F7 · AlphaFold monomer V2.0 prediction for L-threonine 3-dehydrogenase, mitochondrial (Q8K3F7) · 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 Q8K3F7
Elsewhere: RCSB PDB 4YR9 · PDBe 4YR9 · UniProt Q8K3F7

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