MolNFT v1 · #81851 · protein
Structure of a monoclonal antibody complexed with its MHC-I antigen
3V4U · Anti-MHC-I monoclonal antibody, 64-3-7 H chain: “Structure of a monoclonal antibody complexed with its MHC-I antigen”. X-ray diffraction, 5 pockets (best druggability 0.62). MolNFT v1 #81851 on GenesisL1: 3D structure, binding sites…
- PDB
- 3V4U
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-MHC-I monoclonal antibody, 64-3-7 H chain; Anti-MHC-I monoclonal antibody, 64-3-7 L…
- UniProt
- P01897
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti-MHC-I monoclonal antibody, 64-3-7 H chain | protein | 216 | 7% helix, 56% strand | — |
| L | Anti-MHC-I monoclonal antibody, 64-3-7 L chain | protein | 218 | 7% helix, 52% strand | — |
| P | H-2 class I histocompatibility antigen, L-D alpha chain | protein | 8 | 0% helix, 0% strand | P01897 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.62 | 0.74 | 65 | empty |
| 2 | 106 | 0.37 | 0.74 | 25 | empty |
| 3 | 71 | 0.37 | 0.78 | 15 | empty |
| 4 | 76 | 0.33 | 0.75 | 19 | empty |
| 5 | 86 | 0.32 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1752 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 363 Ų buried · 7 hydrogen bonds · protein-protein
- L–P · 221 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3V4U · Structure of a monoclonal antibody complexed with its MHC-I antigen · the same entry in another collection · chain H against H, TM-score 1.00
- P01897 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, L-D alpha… · a predicted model of the same protein · chain P against A, TM-score 0.54
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 P01897
- Elsewhere: RCSB PDB 3V4U · PDBe 3V4U · UniProt P01897
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