MolNFT v1 · #185531 · protein

Hbc-wt in complex with triton X-100

7PZK · Capsid protein: “Hbc-wt in complex with triton X-100”. Electron microscopy, 1 ligand (TRT), 8 pockets (best druggability 0.79). MolNFT v1 #185531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PZK
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 0.79

Structure

electron microscopy · 1 distinct chain · 65% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C, D	Capsid protein	protein	143	65% 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	143	0.79	0.95	27	empty
2	192	0.70	0.87	22	TRT
3	194	0.69	0.86	23	TRT
4	181	0.69	0.87	25	TRT
5	191	0.67	0.85	23	TRT

Interfaces

4 interfaces between chains.

B–A · 2095 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 2009 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 694 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 14 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7PZK · HBc-WT in complex with Triton 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 7PZK · PDBe 7PZK · UniProt P03146

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