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Cryoem structure of type II secretion system secretin gspd in E.COLI K12

Analyse Cryoem structure of type II secretion system secretin gspd in E.COLI K12 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WQ7
Type: protein
Length: 7,080 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative type II secretion system protein D
UniProt: P45758
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 27% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	Putative type II secretion system protein D	protein	472	27% helix, 40% strand	P45758

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	1177	0.88	0.88	124	empty
2	933	0.87	0.88	95	empty
3	650	0.84	0.88	72	empty
4	606	0.84	0.88	66	empty
5	594	0.83	0.88	62	empty

Interfaces

30 interfaces between chains.

G–H · 5184 Å² buried · 78 hydrogen bonds · protein-protein
I–J · 5183 Å² buried · 78 hydrogen bonds · protein-protein
F–G · 5181 Å² buried · 78 hydrogen bonds · protein-protein
A–B · 5179 Å² buried · 78 hydrogen bonds · protein-protein
H–I · 5179 Å² buried · 78 hydrogen bonds · protein-protein

Compared structures

5WQ7 · CryoEM structure of type II secretion system secretin GspD in E.coli K12 · the same entry in another collection · chain O against O, 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 P45758
Elsewhere: RCSB PDB 5WQ7 · PDBe 5WQ7 · UniProt P45758

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