Research workbench
Crystal structure of HLA-A2-WT1-rmf and Fab 11D06
Analyse Crystal structure of HLA-A2-WT1-rmf and Fab 11D06 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BBG
- Type
- protein
- Length
- 810 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class I antigen; Beta-2-microglobulin; Wilms tumor 1 (WT1) derived peptide; Heavy…
- UniProt
- Q861F7, P61769
- Ligands
- NA
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class I antigen | protein | 274 | 26% helix, 39% strand | Q861F7 |
| B | Beta-2-microglobulin | protein | 100 | 0% helix, 49% strand | P61769 |
| C | Wilms tumor 1 (WT1) derived peptide | protein | 9 | 0% helix, 0% strand | — |
| H | Heavy chain of Fab fragment 11D06 | protein | 215 | 7% helix, 50% strand | — |
| L | Light chain of Fab fragment 11D06 | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 5 copies · chains A, C, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.69 | 0.77 | 61 | empty |
| 2 | 93 | 0.68 | 0.92 | 28 | empty |
| 3 | 316 | 0.54 | 0.75 | 41 | empty |
| 4 | 51 | 0.49 | 0.87 | 20 | NA |
| 5 | 162 | 0.47 | 0.76 | 24 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1722 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1403 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 941 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 576 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 330 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
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 Q861F7
- Every structure of UniProt P61769
- Elsewhere: RCSB PDB 7BBG · PDBe 7BBG · UniProt Q861F7 · UniProt P61769
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