MolNFT v1 · #179126 · protein

Satellite phage P4 procapsid including size determination (sid) protein

7JW1 · Major capsid protein gpn: “Satellite phage P4 procapsid including size determination (sid) protein”. Electron microscopy, 20 pockets (best druggability 0.77). MolNFT v1 #179126 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7JW1
Type: protein
Length: 2,858 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein gpn; Size determination protein sid
UniProt: P25477, P05461
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · 5 distinct chains · 34% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, a	Major capsid protein gpn	protein	279	27% helix, 25% strand	P25477
B, b	Major capsid protein gpn	protein	327	28% helix, 24% strand	P25477
C, c	Major capsid protein gpn	protein	281	23% helix, 27% strand	P25477
D, d	Major capsid protein gpn	protein	307	25% helix, 24% strand	P25477
E, e	Size determination protein sid	protein	235	74% helix, 0% strand	P05461

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	1028	0.77	0.79	103	empty
2	978	0.76	0.78	100	empty
3	101	0.72	0.94	24	empty
4	970	0.72	0.76	85	empty
5	524	0.72	0.81	59	empty

Interfaces

22 interfaces between chains.

c–d · 2934 Å² buried · 33 hydrogen bonds · protein-protein
C–D · 2880 Å² buried · 33 hydrogen bonds · protein-protein
D–b · 2777 Å² buried · 32 hydrogen bonds · protein-protein
B–d · 2727 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 2254 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7JW1 · Satellite phage P4 procapsid including size determination (Sid) protein · 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 P25477
Every structure of UniProt P05461
Elsewhere: RCSB PDB 7JW1 · PDBe 7JW1 · UniProt P25477 · UniProt P05461

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