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Cryo-EM structure of vaccinia virus scaffolding protein D13 with N- terminal 17 residue truncation

Analyse Cryo-EM structure of vaccinia virus scaffolding protein D13 with N- terminal 17… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VFF
Type: protein
Length: 1,581 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scaffold protein D13
UniProt: P68440
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 17% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Scaffold protein D13	protein	527	17% helix, 42% strand	P68440

Pockets

20 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	1180	0.84	0.84	118	empty
2	1107	0.83	0.84	103	empty
3	1198	0.83	0.84	117	empty
4	462	0.60	0.75	43	empty
5	223	0.54	0.77	34	empty

Interfaces

3 interfaces between chains.

B–C · 2198 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2192 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 2164 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7VFF · Cryo-EM structure of Vaccinia virus scaffolding protein D13 with N-terminal 17 residue… · 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 P68440
Elsewhere: RCSB PDB 7VFF · PDBe 7VFF · UniProt P68440

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