Research workbench

Cchfv GP38 (IBAR10200)

Analyse Cchfv GP38 (IBAR10200) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VKF
Type: protein
Length: 472 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GP38
UniProt: A0A1V0G0G3
Ligands: NAG
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	GP38	protein	240	20% helix, 35% strand	A0A1V0G0G3
B	GP38	protein	232	21% helix, 32% strand	A0A1V0G0G3

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.53	0.79	41	empty
2	175	0.48	0.76	24	empty
3	78	0.35	0.76	14	empty
4	57	0.29	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 567 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6VKF · CCHFV GP38 (IbAr10200) · 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 A0A1V0G0G3
Elsewhere: RCSB PDB 6VKF · PDBe 6VKF · UniProt A0A1V0G0G3

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