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Structure of a flavodoxin from aquifex aeolicus

Analyse Structure of a flavodoxin from aquifex aeolicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ARK
Type: protein
Length: 1,116 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Flavodoxin
UniProt: O67866
Ligands: PO4
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 43% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Flavodoxin	protein	187	42% helix, 26% strand	O67866
B	Flavodoxin	protein	186	42% helix, 26% strand	O67866
C	Flavodoxin	protein	186	43% helix, 26% strand	O67866
E	Flavodoxin	protein	185	43% helix, 26% strand	O67866
F	Flavodoxin	protein	185	44% helix, 26% strand	O67866

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 6 copies · chains A, B, C, D

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	152	0.83	0.99	21	GOL
2	1109	0.72	0.76	77	empty
3	215	0.51	0.77	24	PO4
4	219	0.50	0.76	28	PO4
5	195	0.50	0.77	28	PO4

Interfaces

10 interfaces between chains.

A–B · 1525 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1507 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 881 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 879 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 859 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 modified (engineered).

Compared structures

2ARK · Structure of a flavodoxin from Aquifex aeolicus · the same entry in another collection · chain F against F, TM-score 1.00
O67866 · AlphaFold monomer V2.0 prediction for flavodoxin (O67866) · a predicted model of the same protein · chain E 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 O67866
Elsewhere: RCSB PDB 2ARK · PDBe 2ARK · UniProt O67866

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