MolNFT v1 · #55450 · protein

Structure of the human line-1 ORF1P trimer

2YKQ: “Structure of the human line-1 ORF1P trimer”. X-ray diffraction, 1 ligand (CL), 8 pockets (best druggability 0.75). MolNFT v1 #55450 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YKQ
Type: protein
Length: 598 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Line-1 ORF1P
UniProt: Q15605
Ligands: CL
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Line-1 ORF1P	protein	200	52% helix, 18% strand	Q15605
B	Line-1 ORF1P	protein	198	51% helix, 17% strand	Q15605
C	Line-1 ORF1P	protein	200	53% helix, 20% strand	Q15605

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	593	0.75	0.82	74	empty
2	305	0.56	0.76	35	empty
3	216	0.53	0.77	24	empty
4	237	0.50	0.75	24	empty
5	202	0.49	0.76	24	empty

Interfaces

3 interfaces between chains.

A–C · 1308 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1231 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1160 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

2YKQ · Structure of the human LINE-1 ORF1p trimer · 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 Q15605
Elsewhere: RCSB PDB 2YKQ · PDBe 2YKQ · UniProt Q15605

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