MolNFT v1 · #112580 · protein

Crystal structure of the heterodimeric hif-2A:ARNT complex with proflavine

4ZPH · Aryl hydrocarbon receptor nuclear translocator: “Crystal structure of the heterodimeric hif-2A:ARNT complex with proflavine”. X-ray diffraction, 1 ligand (PRL), 13 pockets (best druggability 0.77). MolNFT v1 #112580 on GenesisL1: 3D…

PDB: 4ZPH
Type: protein
Length: 1,092 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aryl hydrocarbon receptor nuclear translocator; Endothelial pas domain-containing protein…
UniProt: P53762, P97481
Ligands: PRL
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Aryl hydrocarbon receptor nuclear translocator	protein	254	36% helix, 33% strand	P53762
B	Endothelial pas domain-containing protein 1	protein	292	33% helix, 28% strand	P97481
C	Aryl hydrocarbon receptor nuclear translocator	protein	252	35% helix, 34% strand	P53762
D	Endothelial pas domain-containing protein 1	protein	294	34% helix, 30% strand	P97481

Ligands and binding sites

PRL · Proflavin · ligand · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	93	0.77	0.98	29	empty
2	580	0.75	0.82	68	empty
3	625	0.74	0.81	89	empty
4	50	0.74	0.99	20	empty
5	322	0.73	0.85	31	empty

Interfaces

3 interfaces between chains.

A–B · 3600 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 3491 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 408 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4ZPH · Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with Proflavine · the same entry in another collection · chain B against B, TM-score 1.00
P97481 · AlphaFold monomer V2.0 prediction for endothelial pas domain- containing protein 1… · a predicted model of the same protein · chain D against A, TM-score 0.95
P53762 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain C against A, TM-score 0.85

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 P53762
Every structure of UniProt P97481
Elsewhere: RCSB PDB 4ZPH · PDBe 4ZPH · UniProt P53762 · UniProt P97481

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