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The quasi-atomic model of the adenovirus type 3 penton base dodecahedron

Analyse The quasi-atomic model of the adenovirus type 3 penton base dodecahedron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C9G
Type: protein
Length: 2,235 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penton protein
UniProt: P03276
Pockets: 20 · best druggability 0.91

Structure

electron microscopy · 1 distinct chain · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Penton protein	protein	447	15% helix, 33% strand	P03276

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1000	0.91	0.93	182	empty
2	609	0.84	0.89	71	empty
3	215	0.80	0.94	41	empty
4	204	0.80	0.94	43	empty
5	180	0.80	0.95	39	empty

Interfaces

5 interfaces between chains.

A–B · 3088 Å² buried · 35 hydrogen bonds · protein-protein
A–E · 3088 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 3087 Å² buried · 35 hydrogen bonds · protein-protein
D–E · 3078 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 3074 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

2C9G · The quasi-atomic model of the adenovirus type 3 penton base dodecahedron · the same entry in another collection · chain C against C, 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 P03276
Elsewhere: RCSB PDB 2C9G · PDBe 2C9G · UniProt P03276

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