Research workbench

Vibrio vulnificus epsd

Analyse Vibrio vulnificus epsd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6I1Y
Type: protein
Length: 7,440 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: General secretion pathway protein gspd
UniProt: A0A087IFK6
Pockets: 20 · best druggability 0.74

Structure

electron microscopy · 1 distinct chain · 29% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	General secretion pathway protein gspd	protein	496	29% helix, 38% strand	A0A087IFK6

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	748	0.74	0.80	152	empty
2	215	0.72	0.88	31	empty
3	208	0.72	0.88	31	empty
4	234	0.71	0.86	32	empty
5	240	0.71	0.86	35	empty

Interfaces

30 interfaces between chains.

G–H · 6031 Å² buried · 80 hydrogen bonds · protein-protein
K–L · 6029 Å² buried · 80 hydrogen bonds · protein-protein
B–C · 6025 Å² buried · 79 hydrogen bonds · protein-protein
J–K · 6024 Å² buried · 78 hydrogen bonds · protein-protein
M–N · 6024 Å² buried · 80 hydrogen bonds · protein-protein

Compared structures

6I1Y · Vibrio vulnificus EpsD · 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 A0A087IFK6
Elsewhere: RCSB PDB 6I1Y · PDBe 6I1Y · UniProt A0A087IFK6

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