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T=3 recombinant capsid of semv cp

Analyse T=3 recombinant capsid of semv cp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1X33
Type: protein
Length: 618 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coat protein
UniProt: Q9EB06
Ligands: CA
Pockets: 2 · best druggability 0.41

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coat protein	protein	196	22% helix, 38% strand	Q9EB06
B	Coat protein	protein	197	20% helix, 37% strand	Q9EB06
C	Coat protein	protein	225	20% helix, 37% strand	Q9EB06

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains B, C, A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.41	0.75	32	empty
2	55	0.32	0.76	16	empty

Interfaces

3 interfaces between chains.

B–C · 1003 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 978 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 972 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1X33 · T=3 recombinant capsid of SeMV CP · 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 Q9EB06
Elsewhere: RCSB PDB 1X33 · PDBe 1X33 · UniProt Q9EB06

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