Research workbench

W57A apoflavodoxin from anabaena

Analyse W57A apoflavodoxin from anabaena in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DX9
Type: protein
Length: 672 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavodoxin
UniProt: P0A3E0
Ligands: SO4
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Flavodoxin	protein	168	33% helix, 20% strand	P0A3E0

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

6 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	940	0.75	0.78	112	empty
2	487	0.71	0.81	41	SO4
3	318	0.65	0.80	33	SO4
4	63	0.41	0.81	16	SO4
5	80	0.38	0.78	22	SO4

Interfaces

5 interfaces between chains.

A–B · 301 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 300 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 285 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 269 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 267 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1DX9 · W57A Apoflavodoxin from Anabaena · the same entry in another collection · chain D against D, TM-score 1.00
P0A3E0 · AlphaFold monomer V2.0 prediction for flavodoxin (P0A3E0) · a predicted model of the same protein · chain B 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 P0A3E0
Elsewhere: RCSB PDB 1DX9 · PDBe 1DX9 · UniProt P0A3E0

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