MolNFT v1 · #172862 · protein

HAD7 knob in complex with 3 EC2-EC3 modules of dsg-2

7AGF · Fiber: “HAD7 knob in complex with 3 EC2-EC3 modules of dsg-2”. Electron microscopy, 12 pockets (best druggability 0.81). MolNFT v1 #172862 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7AGF
Type: protein
Length: 1,287 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiber; Desmoglein-2
UniProt: Q5EY45, Q14126
Pockets: 12 · best druggability 0.81

Structure

electron microscopy · 2 distinct chains · 6% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Fiber	protein	198	11% helix, 40% strand	Q5EY45
D, E, F	Desmoglein-2	protein	231	1% helix, 35% strand	Q14126

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	594	0.81	0.86	40	empty
2	986	0.79	0.80	107	empty
3	1147	0.77	0.79	106	empty
4	770	0.77	0.81	77	empty
5	258	0.59	0.79	28	empty

Interfaces

12 interfaces between chains.

A–C · 1063 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1062 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1061 Å² buried · 11 hydrogen bonds · protein-protein
F–B · 469 Å² buried · 7 hydrogen bonds · protein-protein
D–C · 468 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7AGF · HAd7 knob in complex with 3 EC2-EC3 modules of DSG-2 · the same entry in another collection · chain C against C, TM-score 1.00
Q14126 · AlphaFold monomer V2.0 prediction for desmoglein-2 (Q14126) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 Q5EY45
Every structure of UniProt Q14126
Elsewhere: RCSB PDB 7AGF · PDBe 7AGF · UniProt Q5EY45 · UniProt Q14126

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