MolNFT v1 · #189425 · protein

Cryo-EM structure of vaccinia virus scaffolding protein D13

7VFD · Scaffold protein D13: “Cryo-EM structure of vaccinia virus scaffolding protein D13”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #189425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VFD
Type: protein
Length: 1,623 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, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Scaffold protein D13	protein	541	17% helix, 40% 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	1099	0.84	0.85	106	empty
2	707	0.79	0.84	67	empty
3	745	0.79	0.83	75	empty
4	1043	0.75	0.78	80	empty
5	1071	0.75	0.77	83	empty

Interfaces

3 interfaces between chains.

A–C · 2993 Å² buried · 32 hydrogen bonds · protein-protein
B–C · 2992 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2983 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

7VFD · Cryo-EM structure of Vaccinia virus scaffolding protein D13 · 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 7VFD · PDBe 7VFD · UniProt P68440

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