MolNFT v1 · #128303 · protein
868 TCR specific for HLA A02 presenting HIV epitope slyntvatl
5NMD · Human T-cell receptor alpha chain: “868 TCR specific for HLA A02 presenting HIV epitope slyntvatl”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.79). MolNFT v1 #128303 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NMD
- Type
- protein
- Length
- 884 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human T-cell receptor alpha chain; Human T-cell receptor, beta chain
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Human T-cell receptor alpha chain | protein | 200 | 5% helix, 47% strand | — |
| B, D | Human T-cell receptor, beta chain | protein | 242 | 7% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.79 | 0.87 | 67 | EDO |
| 2 | 652 | 0.75 | 0.81 | 74 | empty |
| 3 | 295 | 0.71 | 0.85 | 44 | EDO |
| 4 | 115 | 0.53 | 0.82 | 21 | empty |
| 5 | 110 | 0.40 | 0.75 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2161 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2099 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 965 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5NMD · 868 TCR Specific for HLA A02 presenting HIV Epitope SLYNTVATL · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5NMD · PDBe 5NMD
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