MolNFT v1 · #154854 · protein

Crystal structure of SNX11-pxe domain in dimer form.

6KOI · Sorting nexin-11: “Crystal structure of SNX11-pxe domain in dimer form.”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #154854 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KOI
Type: protein
Length: 3,162 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sorting nexin-11
UniProt: Q9Y5W9
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 21 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, S	Sorting nexin-11	protein	124	42% helix, 22% strand	Q9Y5W9
B	Sorting nexin-11	protein	140	40% helix, 21% strand	Q9Y5W9
C, G	Sorting nexin-11	protein	126	42% helix, 22% strand	Q9Y5W9
D	Sorting nexin-11	protein	147	39% helix, 19% strand	Q9Y5W9
E, M	Sorting nexin-11	protein	125	42% helix, 23% strand	Q9Y5W9
F	Sorting nexin-11	protein	138	41% helix, 19% strand	Q9Y5W9
H	Sorting nexin-11	protein	144	39% helix, 19% strand	Q9Y5W9
I	Sorting nexin-11	protein	125	42% helix, 24% strand	Q9Y5W9
J	Sorting nexin-11	protein	141	40% helix, 21% strand	Q9Y5W9
K	Sorting nexin-11	protein	117	45% helix, 24% strand	Q9Y5W9
L	Sorting nexin-11	protein	143	41% helix, 19% strand	Q9Y5W9
N	Sorting nexin-11	protein	141	40% helix, 21% strand	Q9Y5W9
O	Sorting nexin-11	protein	118	44% helix, 25% strand	Q9Y5W9
P	Sorting nexin-11	protein	141	40% helix, 21% strand	Q9Y5W9
Q	Sorting nexin-11	protein	122	43% helix, 22% strand	Q9Y5W9
R	Sorting nexin-11	protein	139	41% helix, 20% strand	Q9Y5W9
T	Sorting nexin-11	protein	143	40% helix, 20% strand	Q9Y5W9
U	Sorting nexin-11	protein	121	44% helix, 23% strand	Q9Y5W9
V	Sorting nexin-11	protein	130	44% helix, 19% strand	Q9Y5W9
W	Sorting nexin-11	protein	121	44% helix, 24% strand	Q9Y5W9
X	Sorting nexin-11	protein	141	41% helix, 21% strand	Q9Y5W9

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	779	0.79	0.82	66	empty
2	591	0.78	0.84	49	empty
3	724	0.77	0.82	63	empty
4	629	0.76	0.82	50	empty
5	554	0.76	0.83	53	empty

Interfaces

54 interfaces between chains.

I–J · 1419 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 1408 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1401 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1389 Å² buried · 21 hydrogen bonds · protein-protein
M–N · 1365 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified, 12 disulfide (engineered, disulfide).

Compared structures

6KOI · Crystal structure of SNX11-PXe domain in dimer form. · the same entry in another collection · chain K against K, 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 Q9Y5W9
Elsewhere: RCSB PDB 6KOI · PDBe 6KOI · UniProt Q9Y5W9

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