MolNFT v1 · #134389 · protein

Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)

5T2P: “Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01)”. X-ray diffraction, 2 ligands (K89, CL), 12 pockets (best druggability 0.67). MolNFT v1 #134389 on GenesisL1: 3D structure, binding sites and…

PDB: 5T2P
Type: protein
Length: 898 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core protein
UniProt: L7R9I1
Ligands: K89, CL
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Core protein	protein	148	70% helix, 0% strand	L7R9I1
B, D	Core protein	protein	155	67% helix, 0% strand	L7R9I1
C	Core protein	protein	142	68% helix, 0% strand	L7R9I1
E	Core protein	protein	150	67% helix, 0% strand	L7R9I1
F	Core protein	protein	148	67% helix, 0% strand	L7R9I1

Ligands and binding sites

K89 · 4-fluoranyl-3-(4-oxidanylpiperidin-1-yl)sulfonyl-~{N}-[3,4,5-tris(fluoranyl)phenyl]benzamide · ligand · 6 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 5 copies · chains C, D, E, F
IPA · Isopropyl alcohol · additive · 10 copies · chains A, B, C, D, E, F
GOL · Glycerol · additive · 3 copies · chains B, C, D, E
DMS · Dimethyl sulfoxide · additive · 2 copies · chains B, C

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

Pockets

12 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	238	0.67	0.84	29	K89
2	249	0.67	0.83	28	K89
3	229	0.65	0.83	29	K89
4	127	0.60	0.85	33	IPA
5	74	0.54	0.86	17	empty

Interfaces

8 interfaces between chains.

E–F · 2093 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 2018 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1925 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 557 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 553 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5T2P · Hepatitis B virus core protein Y132A mutant in complex with sulfamoylbenzamide (SBA_R01) · 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 5T2P · PDBe 5T2P · UniProt L7R9I1

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