Research workbench
Crystal structure of human CD8AA-MR1-ac-6-fp complex
Analyse Crystal structure of human CD8AA-MR1-ac-6-fp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UMG
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin…
- UniProt
- Q95460, P61769, P01732
- Ligands
- 30W, PO4, CL
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 266 | 29% helix, 41% strand | Q95460 |
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P61769 |
| C | T-cell surface glycoprotein CD8 alpha chain | protein | 113 | 3% helix, 45% strand | P01732 |
| D | T-cell surface glycoprotein CD8 alpha chain | protein | 112 | 3% helix, 47% strand | P01732 |
Ligands and binding sites
- 30W · N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.86 | 0.87 | 110 | empty |
| 2 | 207 | 0.66 | 0.84 | 30 | 30W |
| 3 | 350 | 0.64 | 0.79 | 45 | empty |
| 4 | 54 | 0.59 | 0.91 | 21 | empty |
| 5 | 134 | 0.44 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1319 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 928 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 153 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7UMG · Crystal structure of human CD8aa-MR1-Ac-6-FP complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P01732 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 alpha chain (P01732) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q95460
- Every structure of UniProt P61769
- Every structure of UniProt P01732
- Elsewhere: RCSB PDB 7UMG · PDBe 7UMG · UniProt Q95460 · UniProt P61769 · UniProt P01732
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