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Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map

Analyse Comparative Model of SGIV Major Coat Protein (MCP) Trimer Based on Cryo-EM Map in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OJN
Type: protein
Length: 1,269 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 8.6
Source: Singapore grouper iridovirus
Molecule: Major capsid protein
UniProt: Q5YFJ3
Pockets: 20 · best druggability 0.76

Structure

electron microscopy · resolution 8.6 · 1 distinct chain · 8% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Major capsid protein	protein	423	8% helix, 22% strand	Q5YFJ3

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	471	0.76	0.84	67	empty
2	249	0.74	0.87	51	empty
3	414	0.73	0.83	60	empty
4	359	0.72	0.84	56	empty
5	53	0.71	0.97	18	empty

Interfaces

3 interfaces between chains.

A–C · 1783 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 1716 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1634 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

6OJN · Comparative model of sgiv major coat protein (mcp) trimer based on cryo-EM MAP · 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 Q5YFJ3
Elsewhere: RCSB PDB 6OJN · PDBe 6OJN · UniProt Q5YFJ3

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