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Structure of pdpa-vgrg complex, lidless

Analyse Structure of pdpa-vgrg complex, lidless in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6U9E
Type: protein
Length: 2,148 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pdpa; Vgrg
UniProt: Q7X3I9, Q7X3I8
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 7% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Pdpa	protein	583	8% helix, 27% strand	Q7X3I9
B, D, F	Vgrg	protein	133	0% helix, 50% strand	Q7X3I8

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	360	0.85	0.94	40	empty
2	154	0.77	0.94	24	empty
3	830	0.77	0.81	75	empty
4	153	0.77	0.94	25	empty
5	155	0.77	0.94	25	empty

Interfaces

12 interfaces between chains.

A–E · 3751 Å² buried · 48 hydrogen bonds · protein-protein
A–C · 3723 Å² buried · 44 hydrogen bonds · protein-protein
C–E · 3664 Å² buried · 48 hydrogen bonds · protein-protein
B–D · 3106 Å² buried · 51 hydrogen bonds · protein-protein
D–F · 3106 Å² buried · 45 hydrogen bonds · protein-protein

Compared structures

6U9E · Structure of PdpA-VgrG Complex, Lidless · 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 Q7X3I9
Every structure of UniProt Q7X3I8
Elsewhere: RCSB PDB 6U9E · PDBe 6U9E · UniProt Q7X3I9 · UniProt Q7X3I8

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