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AVR2

Analyse AVR2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WBI
Type: protein
Length: 970 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin-related protein 2
UniProt: P56732
Ligands: BTN, SO4
Pockets: 17 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Avidin-related protein 2	protein	123	7% helix, 49% strand	P56732
B, G	Avidin-related protein 2	protein	120	8% helix, 50% strand	P56732
C, D, E	Avidin-related protein 2	protein	121	7% helix, 50% strand	P56732
H	Avidin-related protein 2	protein	121	7% helix, 50% strand	P56732

Ligands and binding sites

BTN · Biotin · ligand · 8 copies · chains A, D, B, C, E, F, G, H
SO4 · Sulfate ion · ion · 14 copies · chains A, C, B, D, E, H, F, G
GOL · Glycerol · additive · 6 copies · chains A, B, C, F, E, G

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

Pockets

17 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	85	0.68	0.92	23	BTN
2	94	0.67	0.91	25	BTN
3	94	0.66	0.91	25	BTN
4	87	0.66	0.91	25	BTN
5	96	0.66	0.90	24	BTN

Interfaces

13 interfaces between chains.

B–D · 1779 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1759 Å² buried · 22 hydrogen bonds · protein-protein
F–G · 1756 Å² buried · 23 hydrogen bonds · protein-protein
E–H · 1744 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 589 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

1WBI · AVR2 · the same entry in another collection · chain H against H, TM-score 1.00
P56732 · AlphaFold monomer V2.0 prediction for avidin-related protein 2 (P56732) · a predicted model of the same protein · chain H against A, TM-score 0.96

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 P56732
Elsewhere: RCSB PDB 1WBI · PDBe 1WBI · UniProt P56732

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