Research workbench

Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium spinosum

Analyse Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OXM
Type: protein
Length: 808 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.25
Source: Verrucomicrobium spinosum
Molecule: Diaminopimelate aminotransferase
EC: 2.6.1.83
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.25 · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Diaminopimelate aminotransferase (EC 2.6.1.83)	protein	404	45% helix, 16% strand	—

Pockets

9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.78	0.82	68	empty
2	750	0.77	0.81	64	empty
3	90	0.76	0.98	23	empty
4	72	0.74	0.99	22	empty
5	198	0.64	0.84	28	empty

Interfaces

1 interface between chains.

A–B · 3371 Å² buried · 58 hydrogen bonds · protein-protein

Compared structures

6OXM · Crystal structure of L,L-diaminopimelate aminotransferase (dapl) from verrucomicrobium… · 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
Elsewhere: RCSB PDB 6OXM · PDBe 6OXM

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