Research workbench

Yfde from escherichia COLI

Analyse Yfde from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HL6
Type: protein
Length: 2,249 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein yfde
UniProt: P76518
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	Uncharacterized protein yfde	protein	375	41% helix, 15% strand	P76518
B	Uncharacterized protein yfde	protein	376	41% helix, 16% strand	P76518
D, E	Uncharacterized protein yfde	protein	374	41% helix, 15% strand	P76518

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.76	0.98	23	empty
2	75	0.75	0.98	21	empty
3	69	0.75	0.98	22	empty
4	66	0.75	0.98	18	empty
5	417	0.74	0.84	52	empty

Interfaces

10 interfaces between chains.

A–B · 5278 Å² buried · 47 hydrogen bonds · protein-protein
C–D · 5260 Å² buried · 45 hydrogen bonds · protein-protein
E–F · 5199 Å² buried · 43 hydrogen bonds · protein-protein
D–E · 685 Å² buried · 4 hydrogen bonds · protein-protein
C–F · 434 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4HL6 · YfdE from Escherichia coli · the same entry in another collection · chain F against F, TM-score 1.00
P76518 · AlphaFold monomer V2.0 prediction for acetyl-COA:OXALATE CoA- transferase (P76518) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P76518
Elsewhere: RCSB PDB 4HL6 · PDBe 4HL6 · UniProt P76518

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