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Cryo-EM structure of vaccinia virus scaffolding protein D13 with N- terminal polyhistidine tag

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

PDB: 7VFE
Type: protein
Length: 1,587 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scaffold protein D13
UniProt: P68440
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 16% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Scaffold protein D13	protein	529	16% helix, 41% strand	P68440

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	604	0.79	0.85	59	empty
2	595	0.78	0.84	60	empty
3	875	0.77	0.80	75	empty
4	1054	0.75	0.77	90	empty
5	1084	0.74	0.77	88	empty

Interfaces

3 interfaces between chains.

A–B · 2214 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 2209 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 2208 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

7VFE · Cryo-EM structure of Vaccinia virus scaffolding protein D13 with N-terminal polyhistidine… · the same entry in another collection · chain C against C, 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 7VFE · PDBe 7VFE · UniProt P68440

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