MolNFT v1 · #31542 · protein

Crystal structure of the unliganded E2 DNA binding domain from HPV6A

2AYE · Regulatory protein E2: “Crystal structure of the unliganded E2 DNA binding domain from HPV6A”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.58). MolNFT v1 #31542 on GenesisL1: 3D structure, binding sites and…

PDB: 2AYE
Type: protein
Length: 520 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulatory protein E2
UniProt: Q84294
Ligands: SO4
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Regulatory protein E2	protein	86	35% helix, 31% strand	Q84294
B, C, D, E	Regulatory protein E2	protein	87	34% helix, 31% strand	Q84294

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 5 copies · chains B, A, C, D, E, F

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

Pockets

2 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	376	0.58	0.75	47	empty
2	167	0.48	0.77	23	empty

Interfaces

7 interfaces between chains.

E–F · 1390 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1307 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1292 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 415 Å² buried · 5 hydrogen bonds · protein-protein
B–E · 262 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

2AYE · Crystal structure of the unliganded E2 DNA Binding Domain from HPV6a · 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 Q84294
Elsewhere: RCSB PDB 2AYE · PDBe 2AYE · UniProt Q84294

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