MolNFT v1 · #150037 · protein

Structure of a dc-sign crd in complex with high affinity glycomimetic.

6GHV · CD209 antigen: “Structure of a dc-sign crd in complex with high affinity glycomimetic.”. X-ray diffraction, 3 ligands (EZ8, CA, CL), 6 pockets (best druggability 0.78). MolNFT v1 #150037 on GenesisL1: 3D structure, binding sites and…

PDB: 6GHV
Type: protein
Length: 795 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD209 antigen
UniProt: Q9NNX6
Ligands: EZ8, CA, CL
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	CD209 antigen	protein	132	22% helix, 30% strand	Q9NNX6
C, D, E	CD209 antigen	protein	133	23% helix, 34% strand	Q9NNX6

Ligands and binding sites

EZ8 · [1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S}, 4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium · ligand · 6 copies · chains A, D, B, C, E, F
CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F
CL · Chloride ion · ion · 14 copies · chains A, C, B, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1091	0.78	0.80	97	CL, EZ8
2	1108	0.78	0.80	89	CL, EZ8
3	133	0.58	0.84	34	empty
4	83	0.37	0.76	14	empty
5	71	0.36	0.77	13	empty

Interfaces

9 interfaces between chains.

B–E · 489 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 485 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 455 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 438 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 430 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

6GHV · Structure of a DC-SIGN CRD in complex with high affinity glycomimetic. · the same entry in another collection · chain F against F, TM-score 1.00
Q9NNX6 · AlphaFold monomer V2.0 prediction for CD209 antigen (Q9NNX6) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9NNX6
Elsewhere: RCSB PDB 6GHV · PDBe 6GHV · UniProt Q9NNX6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.