MolNFT v1 · #159417 · protein

Structure of 1B1 bound to mouse CD1D

6OOR · Antigen-presenting glycoprotein CD1D1: “Structure of 1B1 bound to mouse CD1D”. X-ray diffraction, 2 ligands (UNL, NA), 11 pockets (best druggability 0.86). MolNFT v1 #159417 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6OOR
Type: protein
Length: 807 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Antibody 1B1 light chain…
UniProt: A0A0R4J090, P01887, A0A0G2JZW1
Ligands: UNL, NA
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D1	protein	273	25% helix, 42% strand	A0A0R4J090
B	Beta-2-microglobulin	protein	99	0% helix, 51% strand	P01887
L	Antibody 1B1 light chain	protein	219	6% helix, 49% strand	A0A0G2JZW1
H	Antibody 1B1 heavy chain	protein	216	6% helix, 50% strand	—

Ligands and binding sites

UNL · Unknown ligand · ligand · 3 copies · chains A, H
NA · Sodium ion · metal · 4 copies · chains A, B, L, H

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	629	0.86	0.90	65	UNL
2	324	0.62	0.79	37	empty
3	289	0.50	0.73	42	empty
4	169	0.49	0.77	23	empty
5	71	0.45	0.82	30	empty

Interfaces

4 interfaces between chains.

L–H · 1990 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1302 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 614 Å² buried · 7 hydrogen bonds · protein-protein
A–L · 59 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6OOR · Structure of 1B1 bound to mouse CD1d · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 A0A0R4J090
Every structure of UniProt P01887
Every structure of UniProt A0A0G2JZW1
Elsewhere: RCSB PDB 6OOR · PDBe 6OOR · UniProt A0A0R4J090 · UniProt P01887 · UniProt A0A0G2JZW1

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