MolNFT v1 · #129918 · protein

HIV integrase binding domain of lens epithelium-derived growth factor

5OYM · PC4 and SFRS1-interacting protein: “HIV integrase binding domain of lens epithelium-derived growth factor”. X-ray diffraction, 8 pockets (best druggability 0.53). MolNFT v1 #129918 on GenesisL1: 3D structure, binding sites and…

PDB: 5OYM
Type: protein
Length: 687 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PC4 and SFRS1-interacting protein
UniProt: O75475
Pockets: 8 · best druggability 0.53

Structure

x-ray diffraction · 5 distinct chains · 73% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A, C	PC4 and SFRS1-interacting protein	protein	85	71% helix, 5% strand	O75475
G	PC4 and SFRS1-interacting protein	protein	88	78% helix, 0% strand	O75475
B	PC4 and SFRS1-interacting protein	protein	84	71% helix, 5% strand	O75475
D, F	PC4 and SFRS1-interacting protein	protein	87	74% helix, 0% strand	O75475
E	PC4 and SFRS1-interacting protein	protein	86	71% helix, 5% strand	O75475

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.53	0.78	39	empty
2	182	0.52	0.78	34	empty
3	146	0.41	0.74	26	empty
4	60	0.41	0.81	15	empty
5	126	0.40	0.75	20	empty

Interfaces

12 interfaces between chains.

E–F · 2313 Å² buried · 5 hydrogen bonds · protein-protein
H–G · 2295 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 2247 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 2223 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 528 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5OYM · HIV Integrase Binding Domain of Lens Epithelium-Derived Growth Factor · the same entry in another collection · chain F against F, TM-score 1.00
O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain B against A, TM-score 0.70

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 O75475
Elsewhere: RCSB PDB 5OYM · PDBe 5OYM · UniProt O75475

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