MolNFT v1 · #139291 · protein

Crystal structure of ycjy from E. COLI

5XB6 · Uncharacterized protein ycjy: “Crystal structure of ycjy from E. COLI”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #139291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XB6
Type: protein
Length: 3,671 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein ycjy
UniProt: P76049
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, K, L	Uncharacterized protein ycjy	protein	306	41% helix, 19% strand	P76049
J	Uncharacterized protein ycjy	protein	305	41% helix, 19% strand	P76049

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	894	0.84	0.86	116	empty
2	901	0.84	0.85	112	empty
3	952	0.80	0.82	114	empty
4	689	0.77	0.82	77	empty
5	94	0.76	0.97	25	empty

Interfaces

18 interfaces between chains.

E–F · 1977 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 1976 Å² buried · 26 hydrogen bonds · protein-protein
K–L · 1974 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1973 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1960 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5XB6 · Crystal structure of YcjY from E. Coli · the same entry in another collection · chain L against L, 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 P76049
Elsewhere: RCSB PDB 5XB6 · PDBe 5XB6 · UniProt P76049

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