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Crystal structure of dnda from streptomyces lividans

Analyse Crystal structure of dnda from streptomyces lividans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VAX
Type: protein
Length: 716 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative uncharacterized protein dnda
UniProt: A7TUX7
Ligands: PLP
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative uncharacterized protein dnda	protein	358	42% helix, 17% strand	A7TUX7

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	924	0.78	0.80	92	PLP
2	902	0.77	0.80	90	PLP
3	198	0.57	0.80	22	empty

Interfaces

1 interface between chains.

A–B · 2061 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

3VAX · Crystal structure of DndA from streptomyces lividans · 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 A7TUX7
Elsewhere: RCSB PDB 3VAX · PDBe 3VAX · UniProt A7TUX7

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