MolNFT v1 · #180092 · protein
CD1A-36:2 sm binary complex
7KOZ · T-cell surface glycoprotein CD1A: “CD1A-36:2 sm binary complex”. X-ray diffraction, 2 ligands (WU7, NAG), 5 pockets (best druggability 0.86). MolNFT v1 #180092 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KOZ
- Type
- protein
- Length
- 377 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A; Beta-2-microglobulin
- UniProt
- P06126, P61769
- Ligands
- WU7, NAG
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A | protein | 273 | 26% helix, 40% strand | P06126 |
| B | Beta-2-microglobulin | protein | 104 | 0% helix, 49% strand | P61769 |
Ligands and binding sites
- WU7 · (4S,7S,17Z)-4-hydroxy-7-[(1S,2E)-1-hydroxyhexadec-2-en-1-yl]-N,N,N-trimethyl-4,9-dioxo-3,5-dioxa-8-aza-4lambda~5~-phosphahexacos-17-en-1-aminium · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.86 | 0.91 | 49 | WU7 |
| 2 | 440 | 0.63 | 0.77 | 45 | EDO |
| 3 | 183 | 0.51 | 0.78 | 38 | EDO |
| 4 | 58 | 0.32 | 0.77 | 22 | empty |
| 5 | 54 | 0.28 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1402 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KOZ · CD1a-36:2 SM binary complex · the same entry in another collection · chain A against A, TM-score 1.00
- P06126 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1A (P06126) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P06126
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7KOZ · PDBe 7KOZ · UniProt P06126 · UniProt P61769
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