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The atomic structure of hadv-F41 at pH 7.4

Analyse The atomic structure of hadv-F41 at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z7N
Type: protein
Length: 11,892 residues
Chains: 36
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-protein VI; Hexon protein; Penton protein; Core-capsid bridging protein…
UniProt: P16139, P11820, Q9QAH8, B5SNS2, Q67716, B5SNR3, P11822
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 32 distinct chains · 11% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Pre-protein VI	protein	12	0% helix, 0% strand	P16139
1	Pre-protein VI	protein	16	0% helix, 13% strand	P16139
2	Pre-protein VI	protein	6	0% helix, 0% strand	P16139
3	Pre-protein VI	protein	12	0% helix, 0% strand	P16139
4	Pre-protein VI	protein	19	0% helix, 11% strand	P16139
5	Pre-protein VI	protein	16	0% helix, 6% strand	P16139
6, 7, 9	Pre-protein VI	protein	3	0% helix, 0% strand	P16139
8	Pre-protein VI	protein	26	0% helix, 0% strand	P16139
A	Hexon protein	protein	788	11% helix, 15% strand	P11820
B	Hexon protein	protein	847	11% helix, 12% strand	P11820
C	Hexon protein	protein	860	8% helix, 14% strand	P11820
D	Hexon protein	protein	887	9% helix, 12% strand	P11820
E	Hexon protein	protein	878	9% helix, 12% strand	P11820
F	Hexon protein	protein	889	12% helix, 15% strand	P11820
G	Hexon protein	protein	880	12% helix, 16% strand	P11820
H	Hexon protein	protein	894	12% helix, 19% strand	P11820
I	Hexon protein	protein	908	14% helix, 20% strand	P11820
J	Hexon protein	protein	907	10% helix, 14% strand	P11820
K	Hexon protein	protein	840	14% helix, 22% strand	P11820
L	Hexon protein	protein	855	11% helix, 22% strand	P11820
M	Penton protein	protein	458	6% helix, 28% strand	Q9QAH8
N	Core-capsid bridging protein	protein	24	0% helix, 8% strand	B5SNS2
O	Pre-hexon-linking protein iiia	protein	267	43% helix, 1% strand	Q67716
P, S	Hexon-interlacing protein	protein	58	0% helix, 5% strand	B5SNR3
Q	Hexon-interlacing protein	protein	50	0% helix, 6% strand	B5SNR3
R	Hexon-interlacing protein	protein	30	0% helix, 3% strand	B5SNR3
T	Pre-hexon-linking protein VIII	protein	178	20% helix, 11% strand	P11822
U	Pre-hexon-linking protein VIII	protein	179	22% helix, 12% strand	P11822
X	Fiber protein	protein	7	0% helix, 0% strand	—
W, Z	Unknown	protein	9	0% helix, 0% strand	—
V	Unknown	protein	10	0% helix, 10% strand	—
Y	Unknown	protein	6	0% helix, 0% strand	—

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	603	0.90	0.96	137	empty
2	1174	0.86	0.87	129	empty
3	503	0.86	0.92	88	empty
4	1047	0.84	0.85	122	empty
5	243	0.82	0.94	34	empty

Interfaces

110 interfaces between chains.

G–I · 8767 Å² buried · 121 hydrogen bonds · protein-protein
D–E · 8597 Å² buried · 132 hydrogen bonds · protein-protein
D–F · 8479 Å² buried · 126 hydrogen bonds · protein-protein
J–K · 8460 Å² buried · 111 hydrogen bonds · protein-protein
H–I · 8436 Å² buried · 121 hydrogen bonds · protein-protein

Compared structures

6Z7N · The atomic structure of HAdV-F41 at pH 7.4 · the same entry in another collection · chain 5 against 5, 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 P16139
Every structure of UniProt P11820
Every structure of UniProt Q9QAH8
Every structure of UniProt B5SNS2
Every structure of UniProt Q67716
Every structure of UniProt B5SNR3
Every structure of UniProt P11822
Elsewhere: RCSB PDB 6Z7N · PDBe 6Z7N · UniProt P16139 · UniProt P11820 · UniProt Q9QAH8 · UniProt B5SNS2 · UniProt Q67716 · UniProt B5SNR3 · UniProt P11822

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