MolNFT v1 · #136988 · protein

Crystal structure of accessory secretion protein 1 and 3

5VAE · Accessory sec system protein ASP1: “Crystal structure of accessory secretion protein 1 and 3”. X-ray diffraction, 20 pockets (best druggability 0.89). MolNFT v1 #136988 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VAE
Type: protein
Length: 2,586 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Accessory sec system protein ASP1; Accessory sec system protein ASP3
UniProt: Q9AET9, Q9AET7
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Accessory sec system protein ASP1	protein	517	35% helix, 25% strand	Q9AET9
B, D, F, H	Accessory sec system protein ASP3	protein	134	0% helix, 44% strand	Q9AET7
C	Accessory sec system protein ASP1	protein	513	34% helix, 25% strand	Q9AET9
E	Accessory sec system protein ASP1	protein	510	35% helix, 25% strand	Q9AET9
G	Accessory sec system protein ASP1	protein	510	33% helix, 25% strand	Q9AET9

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.89	0.91	121	empty
2	759	0.88	0.91	81	empty
3	512	0.86	0.93	68	empty
4	414	0.84	0.92	55	empty
5	458	0.83	0.90	54	empty

Interfaces

8 interfaces between chains.

A–C · 1898 Å² buried · 19 hydrogen bonds · protein-protein
E–G · 1830 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 1778 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1775 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1769 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (engineered).

Compared structures

5VAE · Crystal structure of accessory secretion protein 1 and 3 · the same entry in another collection · chain H against H, TM-score 1.00
Q9AET9 · AlphaFold monomer V2.0 prediction for accessory sec system protein ASP1 (Q9AET9) · a predicted model of the same protein · chain G against A, TM-score 0.97

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 Q9AET9
Every structure of UniProt Q9AET7
Elsewhere: RCSB PDB 5VAE · PDBe 5VAE · UniProt Q9AET9 · UniProt Q9AET7

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