MolNFT v1 · #25420 · protein

Crystal structure of a nipsnap family protein (ATU5224) from agrobacterium tumefaciens str. C58 at 2.40 a resolution

1VQY · Hypothetical protein AGR_PAT_315: “Crystal structure of a nipsnap family protein (ATU5224) from agrobacterium tumefaciens str. C58 at 2.40 a…”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.71). MolNFT v1 #25420…

PDB: 1VQY
Type: protein
Length: 847 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein AGR_PAT_315
UniProt: Q8UK99
Ligands: PO4
Pockets: 12 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F, G, H	Hypothetical protein AGR_PAT_315	protein	105	41% helix, 36% strand	Q8UK99
B	Hypothetical protein AGR_PAT_315	protein	114	39% helix, 33% strand	Q8UK99
D, E	Hypothetical protein AGR_PAT_315	protein	104	42% helix, 37% strand	Q8UK99

Ligands and binding sites

PO4 · Phosphate ion · ion · chains G, H

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

Pockets

12 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	582	0.71	0.80	55	empty
2	545	0.71	0.80	53	empty
3	561	0.71	0.79	56	empty
4	558	0.71	0.80	55	empty
5	596	0.71	0.79	59	empty

Interfaces

20 interfaces between chains.

A–B · 1406 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1378 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 1367 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1359 Å² buried · 25 hydrogen bonds · protein-protein
D–F · 405 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (engineered).

Compared structures

1VQY · CRYSTAL STRUCTURE OF a NIPSNAP FAMILY PROTEIN (ATU5224) FROM AGROBACTERIUM TUMEFACIENS… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q8UK99
Elsewhere: RCSB PDB 1VQY · PDBe 1VQY · UniProt Q8UK99

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