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Crystal structure of probable dehydrogenase TM_0414 from thermotoga maritima

Analyse Crystal structure of probable dehydrogenase TM_0414 from thermotoga maritima in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EZY
Type: protein
Length: 1,328 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dehydrogenase
UniProt: Q9WYP5
Pockets: 10 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dehydrogenase	protein	334	43% helix, 27% strand	Q9WYP5
B	Dehydrogenase	protein	333	43% helix, 26% strand	Q9WYP5
C	Dehydrogenase	protein	330	43% helix, 26% strand	Q9WYP5
D	Dehydrogenase	protein	331	43% helix, 26% strand	Q9WYP5

Ligands and binding sites

MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, D

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.80	0.86	76	empty
2	454	0.67	0.79	47	empty
3	415	0.66	0.79	46	empty
4	375	0.66	0.80	36	empty
5	386	0.66	0.80	39	empty

Interfaces

6 interfaces between chains.

B–C · 1710 Å² buried · 37 hydrogen bonds · protein-protein
A–D · 1678 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 1020 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 990 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 659 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3EZY · Crystal structure of probable dehydrogenase TM_0414 from Thermotoga maritima · the same entry in another collection · chain D against D, TM-score 1.00
Q9WYP5 · AlphaFold monomer V2.0 prediction for myo-inositol 2-dehydrogenase (Q9WYP5) · a predicted model of the same protein · chain B 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 Q9WYP5
Elsewhere: RCSB PDB 3EZY · PDBe 3EZY · UniProt Q9WYP5

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