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Crystal structure of apo AVR4 (D39A/C122S)

Analyse Crystal structure of apo AVR4 (D39A/C122S) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2OF9
Type: protein
Length: 240 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Avidin-related protein 4/5
UniProt: P56734
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Avidin-related protein 4/5	protein	120	8% helix, 50% strand	P56734

Ligands and binding sites

FMT · Formic acid · additive · 15 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	119	0.51	0.80	20	FMT
2	131	0.51	0.80	21	FMT

Interfaces

1 interface between chains.

A–B · 1695 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

2OF9 · Crystal structure of apo AVR4 (D39A/C122S) · the same entry in another collection · chain A against A, TM-score 1.00
P56734 · AlphaFold monomer V2.0 prediction for avidin-related protein 4/5 (P56734) · a predicted model of the same protein · chain A 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 P56734
Elsewhere: RCSB PDB 2OF9 · PDBe 2OF9 · UniProt P56734

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