MolNFT v1 · #165886 · protein

Structure of francisella pdpa-vgrg complex, lidded

6U9F: “Structure of francisella pdpa-vgrg complex, lidded”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #165886 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U9F
Type: protein
Length: 2,550 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pdpa; Vgrg
UniProt: A0Q7H0, A0Q7H3
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 15% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Pdpa	protein	717	18% helix, 26% strand	A0Q7H0
B, D, F	Vgrg	protein	133	0% helix, 51% strand	A0Q7H3

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.86	0.94	40	empty
2	133	0.78	0.96	37	empty
3	857	0.78	0.81	75	empty
4	340	0.78	0.87	62	empty
5	118	0.75	0.95	26	empty

Interfaces

12 interfaces between chains.

A–E · 3906 Å² buried · 50 hydrogen bonds · protein-protein
C–E · 3814 Å² buried · 51 hydrogen bonds · protein-protein
A–C · 3794 Å² buried · 50 hydrogen bonds · protein-protein
B–F · 3123 Å² buried · 60 hydrogen bonds · protein-protein
B–D · 3093 Å² buried · 49 hydrogen bonds · protein-protein

Compared structures

6U9F · Structure of Francisella PdpA-VgrG Complex, Lidded · 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 A0Q7H0
Every structure of UniProt A0Q7H3
Elsewhere: RCSB PDB 6U9F · PDBe 6U9F · UniProt A0Q7H0 · UniProt A0Q7H3

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