Research workbench
Crystal structure of HLA-A68 presenting a C-terminally extended peptide
Analyse Crystal structure of HLA-A68 presenting a C-terminally extended peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EI2
- Type
- protein
- Length
- 385 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-68 alpha chain; Beta-2-microglobulin…
- UniProt
- P01891, P61769, P30279
- Ligands
- NI, CD, CO
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-68 alpha chain | protein | 275 | 26% helix, 40% strand | P01891 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | G1/S-specific cyclin-D2 | protein | 10 | 0% helix, 0% strand | P30279 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A
- CO · Cobalt (II) ion · metal · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.69 | 0.77 | 57 | EDO |
| 2 | 75 | 0.44 | 0.81 | 23 | EDO |
| 3 | 67 | 0.37 | 0.78 | 16 | empty |
| 4 | 82 | 0.37 | 0.77 | 17 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 1312 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 967 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6EI2 · Crystal Structure of HLA-A68 presenting a C-terminally extended peptide · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- P30279 · AlphaFold monomer V2.0 prediction for G1/S-specific cyclin-D2 (P30279) · a predicted model of the same protein · chain C against A, TM-score 0.37
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 P01891
- Every structure of UniProt P61769
- Every structure of UniProt P30279
- Elsewhere: RCSB PDB 6EI2 · PDBe 6EI2 · UniProt P01891 · UniProt P61769 · UniProt P30279
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