MolNFT v1 · #126337 · protein
Crystal structure of murine P14 TCR/ H-2DB complex with pa, modified GP33 peptide from lcmv
5M01 · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of murine P14 TCR/ H-2DB complex with pa, modified GP33 peptide from lcmv”. X-ray diffraction, 12 pockets (best druggability 0.73). MolNFT v1 #126337 on…
- PDB
- 5M01
- Type
- protein
- Length
- 811 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, D-B alpha chain; Beta-2-microglobulin; Protein…
- UniProt
- P01899, P01887, A0A0G2JF94, P01849, P04213, P01851
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 28% helix, 40% strand | P01899 |
| B | Beta-2-microglobulin | protein | 101 | 0% helix, 49% strand | P01887 |
| G | Protein TRAV14-1,T-cell receptor alpha chain C region | protein | 188 | 4% helix, 50% strand | A0A0G2JF94, P01849 |
| H | T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region | protein | 237 | 8% helix, 53% strand | P04213, P01851 |
| P | Lcmv-derived GP33 altered peptide ligand pa | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.73 | 0.77 | 75 | empty |
| 2 | 659 | 0.66 | 0.75 | 52 | empty |
| 3 | 174 | 0.58 | 0.82 | 31 | empty |
| 4 | 172 | 0.58 | 0.82 | 38 | empty |
| 5 | 134 | 0.53 | 0.81 | 27 | GOL |
Interfaces
7 interfaces between chains.
- G–H · 2179 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 23 hydrogen bonds · protein-protein
- A–P · 880 Ų buried · 24 hydrogen bonds · protein-protein
- A–G · 443 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 378 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5M01 · Crystal structure of murine P14 TCR/ H-2Db complex with PA, modified gp33 peptide from… · the same entry in another collection · chain P against P, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01851 · AlphaFold monomer V2.0 prediction for T-cell receptor beta-2 chain C region (P01851) · a predicted model of the same protein · chain H against A, TM-score 0.52
- P04213 · AlphaFold monomer V2.0 prediction for T-cell receptor beta chain V region C5 (P04213) · a predicted model of the same protein · chain H against A, TM-score 0.46
- P01849 · AlphaFold monomer V2.0 prediction for T-cell receptor alpha chain C region (P01849) · a predicted model of the same protein · chain G against A, TM-score 0.41
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 P01899
- Every structure of UniProt P01887
- Every structure of UniProt A0A0G2JF94
- Every structure of UniProt P01849
- Every structure of UniProt P04213
- Every structure of UniProt P01851
- Elsewhere: RCSB PDB 5M01 · PDBe 5M01 · UniProt P01899 · UniProt P01887 · UniProt A0A0G2JF94 · UniProt P01849 · UniProt P04213 · UniProt P01851
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