Research workbench

HBV capsid Y132A with compound 10B at 2.5A resolution

Analyse HBV capsid Y132A with compound 10B at 2.5A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7S76
Type: protein
Length: 800 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: L7R9I1
Ligands: 8EI
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 6 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	138	71% helix, 0% strand	L7R9I1
B	Capsid protein	protein	137	72% helix, 0% strand	L7R9I1
C	Capsid protein	protein	133	73% helix, 0% strand	L7R9I1
D	Capsid protein	protein	133	74% helix, 0% strand	L7R9I1
E	Capsid protein	protein	133	71% helix, 0% strand	L7R9I1
F	Capsid protein	protein	126	70% helix, 0% strand	L7R9I1

Ligands and binding sites

8EI · (1-methyl-1H-1,2,4-triazol-3-yl)methyl {(4S)-1-[(3-chloro-4-fluorophenyl)carbamoyl]-2-methyl-2,4,5,6-tetrahydrocyclopenta[c]pyrrol-4-yl}carbamate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	195	0.67	0.85	31	8EI
2	232	0.66	0.83	29	8EI
3	216	0.65	0.83	29	8EI
4	71	0.58	0.88	24	empty
5	58	0.30	0.75	14	empty

Interfaces

8 interfaces between chains.

A–B · 1979 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1953 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 1761 Å² buried · 20 hydrogen bonds · protein-protein
D–E · 566 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 564 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7S76 · HBV CAPSID Y132A WITH COMPOUND 10b AT 2.5A RESOLUTION · the same entry in another collection · chain A against A, 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 L7R9I1
Elsewhere: RCSB PDB 7S76 · PDBe 7S76 · UniProt L7R9I1

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