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Crystal structure of an hypothetical protein

Analyse Crystal structure of an hypothetical protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VHK
Type: protein
Length: 853 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein yqeu
UniProt: P54461
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein yqeu	protein	235	34% helix, 25% strand	P54461
B	Hypothetical protein yqeu	protein	196	34% helix, 20% strand	P54461
C	Hypothetical protein yqeu	protein	244	36% helix, 24% strand	P54461
D	Hypothetical protein yqeu	protein	178	37% helix, 18% strand	P54461

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	247	0.63	0.81	28	empty
2	246	0.59	0.80	29	empty
3	293	0.57	0.77	31	empty
4	244	0.55	0.77	28	empty
5	195	0.52	0.77	23	empty

Interfaces

3 interfaces between chains.

A–B · 1674 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 1668 Å² buried · 29 hydrogen bonds · protein-protein
B–C · 558 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1VHK · Crystal structure of an hypothetical protein · the same entry in another collection · chain D against D, TM-score 1.00
P54461 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase E… · a predicted model of the same protein · chain C 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 P54461
Elsewhere: RCSB PDB 1VHK · PDBe 1VHK · UniProt P54461

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