MolNFT v1 · #151918 · protein

Aeromonas hydrophila exed

6I1X · Type II secretion system protein D: “Aeromonas hydrophila exed”. Electron microscopy, 20 pockets (best druggability 0.80). MolNFT v1 #151918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6I1X
Type: protein
Length: 7,290 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type II secretion system protein D
UniProt: P31780
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 27% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	Type II secretion system protein D	protein	486	27% helix, 39% strand	P31780

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	1153	0.80	0.81	122	empty
2	510	0.76	0.84	78	empty
3	482	0.75	0.84	70	empty
4	730	0.72	0.78	80	empty
5	663	0.70	0.78	92	empty

Interfaces

31 interfaces between chains.

H–I · 6509 Å² buried · 120 hydrogen bonds · protein-protein
G–H · 6347 Å² buried · 117 hydrogen bonds · protein-protein
A–O · 6227 Å² buried · 107 hydrogen bonds · protein-protein
K–L · 6224 Å² buried · 103 hydrogen bonds · protein-protein
A–B · 6224 Å² buried · 104 hydrogen bonds · protein-protein

Compared structures

6I1X · Aeromonas hydrophila ExeD · 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 P31780
Elsewhere: RCSB PDB 6I1X · PDBe 6I1X · UniProt P31780

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