MolNFT v1 · #28712 · protein
TCR/HLA-DR2B/MBP-peptide complex
1YMM · HLA class II histocompatibility antigen, dr alpha chain: “TCR/HLA-DR2B/MBP-peptide complex”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.52). MolNFT v1 #28712 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1YMM
- Type
- protein
- Length
- 716 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, Q29790, P02686, P01850
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 5 distinct chains · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 182 | 14% helix, 44% strand | P01903 |
| B | HLA class II histocompatibility antigen, dr beta chain | protein | 178 | 22% helix, 41% strand | Q29790 |
| C | Mbp peptide | protein | 14 | 0% helix, 7% strand | P02686 |
| D | T cell receptor alpha chain | protein | 96 | 3% helix, 26% strand | — |
| E | T-cell receptor beta chain | protein | 246 | 3% helix, 29% strand | P01850 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.52 | 0.78 | 30 | empty |
| 2 | 155 | 0.51 | 0.79 | 25 | empty |
| 3 | 295 | 0.50 | 0.73 | 43 | empty |
| 4 | 188 | 0.49 | 0.76 | 30 | empty |
| 5 | 83 | 0.34 | 0.75 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2484 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 785 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 681 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 375 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1YMM · TCR/HLA-DR2b/MBP-peptide complex · the same entry in another collection · chain E against E, TM-score 1.00
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A against A, TM-score 0.95
- P01850 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 1 (P01850) · a predicted model of the same protein · chain E against A, TM-score 0.50
- P02686 · AlphaFold monomer V2.0 prediction for myelin basic protein (P02686) · a predicted model of the same protein · chain C against A, TM-score 0.30
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 P01903
- Every structure of UniProt Q29790
- Every structure of UniProt P02686
- Every structure of UniProt P01850
- Elsewhere: RCSB PDB 1YMM · PDBe 1YMM · UniProt P01903 · UniProt Q29790 · UniProt P02686 · UniProt P01850
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