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Crystal structure of hypothetical protein yedk from escherichia COLI

Analyse Crystal structure of hypothetical protein yedk 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: 2ICU
Type: protein
Length: 423 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein yedk
UniProt: P76318
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein yedk	protein	210	27% helix, 35% strand	P76318
B	Hypothetical protein yedk	protein	213	26% helix, 34% strand	P76318

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.62	0.82	45	empty
2	82	0.54	0.85	18	empty
3	82	0.53	0.85	17	empty

Interfaces

1 interface between chains.

A–B · 439 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

2ICU · Crystal Structure of Hypothetical Protein YedK From Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
P76318 · AlphaFold monomer V2.0 prediction for abasic site processing protein yedk (P76318) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P76318
Elsewhere: RCSB PDB 2ICU · PDBe 2ICU · UniProt P76318

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