MolNFT v1 · #33479 · protein
MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and PBM8 peptide
2CLV · H-2 class I histocompatibility antigen, K-B alpha chain: “MHC class I natural mutant H-2KBM8 heavy chain complexed with beta-2 microglobulin and PBM8 peptide”. X-ray diffraction, 9 pockets (best druggability 0.61). MolNFT v1 #33479…
- PDB
- 2CLV
- Type
- protein
- Length
- 770 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2 microglobulin; RBM5…
- UniProt
- P01901, P01887, Q99KV9
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 28% helix, 38% strand | P01901 |
| B, P | Beta-2 microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, M | RBM5 protein | protein | 8 | 0% helix, 0% strand | Q99KV9 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.61 | 0.74 | 48 | empty |
| 2 | 438 | 0.58 | 0.74 | 49 | empty |
| 3 | 170 | 0.52 | 0.78 | 31 | empty |
| 4 | 167 | 0.52 | 0.79 | 27 | empty |
| 5 | 66 | 0.42 | 0.81 | 16 | empty |
Interfaces
5 interfaces between chains.
- H–P · 1212 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1128 Ų buried · 19 hydrogen bonds · protein-protein
- H–M · 945 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 940 Ų buried · 30 hydrogen bonds · protein-protein
- A–H · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2CLV · MHC Class I Natural Mutant H-2Kbm8 Heavy Chain Complexed With beta-2 Microglobulin and… · the same entry in another collection · chain M against M, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain P against A, TM-score 0.99
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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt Q99KV9
- Elsewhere: RCSB PDB 2CLV · PDBe 2CLV · UniProt P01901 · UniProt P01887 · UniProt Q99KV9
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