MolNFT v1 · #51759 · protein

Structure of the yersinia enterocolitica type III secretion translocator chaperone sycd

2VGX: “Structure of the yersinia enterocolitica type III secretion translocator chaperone sycd”. X-ray diffraction, 4 pockets (best druggability 0.38). MolNFT v1 #51759 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VGX
Type: protein
Length: 279 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chaperone sycd
UniProt: O87496
Pockets: 4 · best druggability 0.38

Structure

x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Chaperone sycd	protein	134	78% helix, 0% strand	O87496
B	Chaperone sycd	protein	145	79% helix, 0% strand	O87496

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.38	0.76	19	empty
2	56	0.31	0.75	12	empty
3	56	0.28	0.74	15	empty
4	53	0.27	0.74	12	empty

Interfaces

1 interface between chains.

A–B · 963 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified (methylation).

Compared structures

2VGX · Structure of the Yersinia enterocolitica Type III Secretion Translocator Chaperone SycD · 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 O87496
Elsewhere: RCSB PDB 2VGX · PDBe 2VGX · UniProt O87496

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