MolNFT v1 · #143999 · protein
2B4 I-ek TCR-MHC complex with affinity-enhancing velcro peptide
6BGA · H-2 class II histocompatibility antigen, E-K alpha chain: “2B4 I-ek TCR-MHC complex with affinity-enhancing velcro peptide”. X-ray diffraction, 3 ligands (NAG, FUC, PO4), 12 pockets (best druggability 0.73). MolNFT v1 #143999 on…
- PDB
- 6BGA
- Type
- protein
- Length
- 839 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class II histocompatibility antigen, E-K alpha chain; 2B4 PEPTIDE,MHC I-ek B chain; T…
- UniProt
- P04224, Q31163
- Ligands
- NAG, FUC, PO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class II histocompatibility antigen, E-K alpha chain | protein | 182 | 14% helix, 47% strand | P04224 |
| B | 2B4 PEPTIDE,MHC I-ek B chain | protein | 207 | 15% helix, 42% strand | Q31163 |
| C | T cell receptor 2B4 alpha chain | protein | 199 | 3% helix, 49% strand | — |
| D | T cell receptor 2B4 beta chain | protein | 245 | 8% helix, 49% strand | — |
| E | Velcro peptide | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.73 | 0.76 | 64 | empty |
| 2 | 171 | 0.46 | 0.75 | 26 | empty |
| 3 | 138 | 0.42 | 0.75 | 21 | empty |
| 4 | 116 | 0.42 | 0.76 | 29 | empty |
| 5 | 109 | 0.37 | 0.74 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 3334 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 2210 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 606 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 457 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 307 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6BGA · 2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P04224 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, E-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P04224
- Every structure of UniProt Q31163
- Elsewhere: RCSB PDB 6BGA · PDBe 6BGA · UniProt P04224 · UniProt Q31163
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