MolNFT v1 · #184337 · protein

Anti-EPHA1 JD1-1 vh domain

7OMN: “Anti-EPHA1 JD1-1 vh domain”. X-ray diffraction, 5 pockets (best druggability 0.57). MolNFT v1 #184337 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7OMN
Type: protein
Length: 372 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: JD1-1 vh domain
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	JD1-1 vh domain	protein	124	10% helix, 50% strand	—

Ligands and binding sites

IMD · Imidazole · additive · 6 copies · chains A, B, C
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.57	0.79	34	GOL, IMD
2	114	0.40	0.75	25	IMD
3	74	0.40	0.79	18	empty
4	65	0.36	0.78	20	IMD
5	53	0.26	0.73	15	IMD

Interfaces

3 interfaces between chains.

B–C · 817 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 580 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 528 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7OMN · Anti-EphA1 JD1-1 VH domain · 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
Elsewhere: RCSB PDB 7OMN · PDBe 7OMN

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.