MolNFT v1 · #114520 · protein
Mage-A3 reactive TCR in complex with mage-A3 in HLA-A1
5BRZ · HLA class I histocompatibility antigen, a-1 alpha chain: “Mage-A3 reactive TCR in complex with mage-A3 in HLA-A1”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.69). MolNFT v1 #114520 on GenesisL1: 3D structure…
- PDB
- 5BRZ
- Type
- protein
- Length
- 822 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class I histocompatibility antigen, a-1 alpha chain; Beta-2-microglobulin…
- UniProt
- P30443, P61769, A0A0B4J279, P01848, A0A578, K7N5M4
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class I histocompatibility antigen, a-1 alpha chain | protein | 275 | 26% helix, 42% strand | P30443 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Glu-val-asp-pro-ile-gly-his-leu-tyr | protein | 9 | 0% helix, 0% strand | — |
| D | Protein TRAV21,T-cell receptor alpha chain C region | protein | 197 | 2% helix, 44% strand | A0A0B4J279, P01848 |
| E | Protein TRBV5-1,HUMAN nkt TCR beta chain | protein | 241 | 7% helix, 52% strand | A0A578, K7N5M4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.69 | 0.75 | 81 | empty |
| 2 | 668 | 0.69 | 0.77 | 64 | empty |
| 3 | 212 | 0.55 | 0.78 | 38 | empty |
| 4 | 81 | 0.45 | 0.81 | 17 | empty |
| 5 | 112 | 0.43 | 0.77 | 18 | empty |
Interfaces
7 interfaces between chains.
- D–E · 2084 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1385 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 913 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 584 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5BRZ · MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1 · the same entry in another collection · chain E against E, 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
- P01848 · AlphaFold monomer V2.0 prediction for T cell receptor alpha chain constant (P01848) · a predicted model of the same protein · chain D against A, TM-score 0.39
- A0A578 · AlphaFold monomer V2.0 prediction for T cell receptor beta variable 5-1 (A0A578) · a predicted model of the same protein · chain E against A, TM-score 0.38
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 P30443
- Every structure of UniProt P61769
- Every structure of UniProt A0A0B4J279
- Every structure of UniProt P01848
- Every structure of UniProt A0A578
- Every structure of UniProt K7N5M4
- Elsewhere: RCSB PDB 5BRZ · PDBe 5BRZ · UniProt P30443 · UniProt P61769 · UniProt A0A0B4J279 · UniProt P01848 · UniProt A0A578 · UniProt K7N5M4
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