Research workbench
Model of the ac-6-FP/HPMR1/BB2M/TAPBPR complex from integrated docking, NMR and restrained md
Analyse Model of the ac-6-FP/HPMR1/BB2M/TAPBPR complex from integrated docking, NMR and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RNO
- Type
- protein
- Length
- 748 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin; Tap…
- UniProt
- Q95460, C1ITJ8, P01888, Q53GH5
- Ligands
- 30W
- Pockets
- 11 · best druggability 0.80
Structure
solution nmr · 3 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major histocompatibility complex class I-related gene protein | protein | 268 | 27% helix, 44% strand | Q95460, C1ITJ8 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 60% strand | P01888 |
| C | Tap binding protein-like variant | protein | 383 | 4% helix, 45% strand | Q53GH5 |
Ligands and binding sites
- 30W · N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.80 | 0.84 | 79 | empty |
| 2 | 1054 | 0.77 | 0.79 | 99 | empty |
| 3 | 459 | 0.74 | 0.83 | 47 | 30W |
| 4 | 68 | 0.72 | 0.97 | 23 | empty |
| 5 | 317 | 0.69 | 0.83 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1771 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1391 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 517 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7RNO · Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated docking, NMR and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q95460 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain A against A, TM-score 0.92
- C1ITJ8 · AlphaFold monomer V2.0 prediction for major histocompatibility complex class I-related… · a predicted model of the same protein · chain A against A, TM-score 0.91
- P01888 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01888) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q95460
- Every structure of UniProt C1ITJ8
- Every structure of UniProt P01888
- Every structure of UniProt Q53GH5
- Elsewhere: RCSB PDB 7RNO · PDBe 7RNO · UniProt Q95460 · UniProt C1ITJ8 · UniProt P01888 · UniProt Q53GH5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.