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Hbc-P5T in complex with X-100

Analyse Hbc-P5T in complex with X-100 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PZM
Type: protein
Length: 572 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: P03146
Ligands: TRT
Pockets: 8 · best druggability 0.78

Structure

electron microscopy · 1 distinct chain · 68% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, D	Capsid protein	protein	143	68% helix, 0% strand	P03146

Ligands and binding sites

TRT · Fragment of triton X-100 · ligand · 4 copies · chains B, A, C, D

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	148	0.78	0.95	28	empty
2	202	0.69	0.86	25	TRT
3	181	0.69	0.87	24	TRT
4	186	0.69	0.86	20	TRT
5	185	0.68	0.86	21	TRT

Interfaces

3 interfaces between chains.

B–A · 2071 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 2045 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 691 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7PZM · HBc-P5T in complex with X-100 · 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 P03146
Elsewhere: RCSB PDB 7PZM · PDBe 7PZM · UniProt P03146

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