MolNFT v1 · #59921 · protein
H-2DB complex with murine GP100
3CCH · H-2 class I histocompatibility antigen, D-B alpha chain: “H-2DB complex with murine GP100”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.79). MolNFT v1 #59921 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CCH
- Type
- protein
- Length
- 1,528 residues
- Chains
- 12
- 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; Nonameric…
- UniProt
- P01899, P01887
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 276 | 26% helix, 40% strand | P01899 |
| B, E, H, K | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F, I, L | Nonameric peptide murine GP100 | protein | 9 | 0% helix, 0% strand | — |
| G, J | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 272 | 24% helix, 38% strand | P01899 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, D, E, G, H, J, K
- GOL · Glycerol · additive · 4 copies · chains A, B, D, E, G, H, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.79 | 0.80 | 108 | GOL |
| 2 | 367 | 0.68 | 0.81 | 55 | SO4 |
| 3 | 498 | 0.66 | 0.77 | 40 | GOL |
| 4 | 309 | 0.63 | 0.80 | 47 | empty |
| 5 | 262 | 0.62 | 0.80 | 38 | GOL |
Interfaces
18 interfaces between chains.
- J–K · 1379 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1355 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1347 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1344 Ų buried · 22 hydrogen bonds · protein-protein
- J–L · 926 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3CCH · H-2Db complex with murine gp100 · the same entry in another collection · chain L against L, TM-score 1.00
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
- Elsewhere: RCSB PDB 3CCH · PDBe 3CCH · UniProt P01899 · UniProt P01887
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