Research workbench

Crystal structure of D-threonine aldolase from filomicrobium marinum

Analyse Crystal structure of D-threonine aldolase from filomicrobium marinum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DIB
Type: protein
Length: 740 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-threonine aldolase
EC: 4.1.2.42
UniProt: A0A0D6JKM4
Pockets: 10 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-threonine aldolase (EC 4.1.2.42)	protein	369	33% helix, 23% strand	A0A0D6JKM4
B	D-threonine aldolase (EC 4.1.2.42)	protein	371	33% helix, 23% strand	A0A0D6JKM4

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	257	0.66	0.83	35	empty
2	117	0.61	0.86	19	empty
3	255	0.60	0.80	32	empty
4	120	0.59	0.85	20	empty
5	261	0.53	0.76	37	empty

Interfaces

1 interface between chains.

A–B · 2393 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (cofactor).

Compared structures

7DIB · Crystal structure of D-threonine aldolase from Filomicrobium marinum · 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 A0A0D6JKM4
Elsewhere: RCSB PDB 7DIB · PDBe 7DIB · UniProt A0A0D6JKM4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.