MolNFT v1 · #81889 · protein

Structure of FBXL5 hemerythrin domain, P2(1) cell

3V5Y · F-BOX/LRR-repeat protein 5: “Structure of FBXL5 hemerythrin domain, P2(1) cell”. X-ray diffraction, 1 ligand (FEO), 7 pockets (best druggability 0.84). MolNFT v1 #81889 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3V5Y
Type: protein
Length: 601 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: F-BOX/LRR-repeat protein 5
UniProt: Q9UKA1
Ligands: FEO
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 86% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	F-BOX/LRR-repeat protein 5	protein	153	85% helix, 0% strand	Q9UKA1
B	F-BOX/LRR-repeat protein 5	protein	148	86% helix, 0% strand	Q9UKA1
C	F-BOX/LRR-repeat protein 5	protein	150	86% helix, 0% strand	Q9UKA1
D	F-BOX/LRR-repeat protein 5	protein	150	86% helix, 0% strand	Q9UKA1

Ligands and binding sites

FEO · Mu-oxo-diiron · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 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	1066	0.84	0.84	87	empty
2	101	0.53	0.83	20	empty
3	153	0.52	0.79	15	empty
4	97	0.46	0.80	24	empty
5	98	0.45	0.79	19	empty

Interfaces

5 interfaces between chains.

A–B · 782 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 405 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 389 Å² buried · 1 hydrogen bond · protein-protein
A–D · 99 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3V5Y · Structure of FBXL5 hemerythrin domain, P2(1) cell · the same entry in another collection · chain D against D, TM-score 1.00
Q9UKA1 · AlphaFold monomer V2.0 prediction for F-BOX/LRR-repeat protein 5 (Q9UKA1) · a predicted model of the same protein · chain B 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 Q9UKA1
Elsewhere: RCSB PDB 3V5Y · PDBe 3V5Y · UniProt Q9UKA1

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