MolNFT v1 · #152801 · protein

Structure of the C-terminal head domain of the avian adenovirus edsv fiber

6ITX · Fiber protein: “Structure of the C-terminal head domain of the avian adenovirus edsv fiber”. X-ray diffraction, 2 ligands (GLN, SO4), 14 pockets (best druggability 0.84). MolNFT v1 #152801 on GenesisL1: 3D structure, binding sites…

PDB: 6ITX
Type: protein
Length: 1,313 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiber protein
UniProt: S4TZM6
Ligands: GLN, SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 8% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fiber protein	protein	219	8% helix, 41% strand	S4TZM6
B	Fiber protein	protein	216	10% helix, 44% strand	S4TZM6
D	Fiber protein	protein	223	6% helix, 41% strand	S4TZM6
C, E	Fiber protein	protein	217	7% helix, 40% strand	S4TZM6
F	Fiber protein	protein	221	9% helix, 41% strand	S4TZM6

Ligands and binding sites

GLN · Glutamine · ligand · 5 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E, F

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	239	0.84	0.96	33	SO4
2	216	0.83	0.97	33	SO4
3	616	0.70	0.79	77	SO4
4	342	0.65	0.80	32	empty
5	372	0.64	0.78	42	GLN

Interfaces

9 interfaces between chains.

D–F · 1101 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 1096 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1049 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 988 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 965 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6ITX · Structure of the C-terminal head domain of the avian adenovirus EDSV fiber · the same entry in another collection · chain D against D, 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 S4TZM6
Elsewhere: RCSB PDB 6ITX · PDBe 6ITX · UniProt S4TZM6

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