Research workbench

Hadv-F41 capsid

Analyse Hadv-F41 capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YBA
Type: protein
Length: 12,388 residues
Chains: 26
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hexon protein; Penton protein; Pre-hexon-linking protein iiia; Pre-hexon-linking protein…
UniProt: B2ZX09, Q9QAH8, Q67716, B5SNS9, B5SNR3, B5SNS4, B5SNS1
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 16 distinct chains · 10% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hexon protein	protein	912	10% helix, 20% strand	B2ZX09
B	Hexon protein	protein	913	8% helix, 19% strand	B2ZX09
C, J	Hexon protein	protein	914	9% helix, 21% strand	B2ZX09
D, I	Hexon protein	protein	908	9% helix, 21% strand	B2ZX09
E	Hexon protein	protein	917	8% helix, 19% strand	B2ZX09
F, G	Hexon protein	protein	910	9% helix, 21% strand	B2ZX09
H	Hexon protein	protein	915	10% helix, 21% strand	B2ZX09
K	Hexon protein	protein	912	10% helix, 20% strand	B2ZX09
L	Hexon protein	protein	911	8% helix, 18% strand	B2ZX09
M	Penton protein	protein	452	11% helix, 27% strand	Q9QAH8
N	Pre-hexon-linking protein iiia	protein	298	44% helix, 4% strand	Q67716
O, P	Pre-hexon-linking protein VIII	protein	180	22% helix, 11% strand	B5SNS9
Q, R, S, T	Hexon-interlacing protein	protein	50	0% helix, 10% strand	B5SNR3
U, V, Y, u	Pre-protein VI	protein	29	0% helix, 7% strand	B5SNS4
W	Pre-histone-like nucleoprotein	protein	6	0% helix, 0% strand	B5SNS1
w	Pre-histone-like nucleoprotein	protein	12	0% helix, 0% strand	B5SNS1

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	1177	0.84	0.85	148	empty
2	806	0.83	0.86	113	empty
3	1168	0.83	0.84	102	empty
4	266	0.82	0.94	31	empty
5	883	0.82	0.84	128	empty

Interfaces

78 interfaces between chains.

H–I · 9050 Å² buried · 112 hydrogen bonds · protein-protein
J–L · 9038 Å² buried · 112 hydrogen bonds · protein-protein
D–E · 8951 Å² buried · 116 hydrogen bonds · protein-protein
G–H · 8929 Å² buried · 110 hydrogen bonds · protein-protein
B–C · 8885 Å² buried · 118 hydrogen bonds · protein-protein

Compared structures

6YBA · HAdV-F41 Capsid · the same entry in another collection · chain B against B, 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 B2ZX09
Every structure of UniProt Q9QAH8
Every structure of UniProt Q67716
Every structure of UniProt B5SNS9
Every structure of UniProt B5SNR3
Every structure of UniProt B5SNS4
Every structure of UniProt B5SNS1
Elsewhere: RCSB PDB 6YBA · PDBe 6YBA · UniProt B2ZX09 · UniProt Q9QAH8 · UniProt Q67716 · UniProt B5SNS9 · UniProt B5SNR3 · UniProt B5SNS4 · UniProt B5SNS1

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