MolNFT v1 · #184735 · protein
Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived GP33 peptide with D- aminoacid
7P0T · H-2 class I histocompatibility antigen, D-B alpha chain: “Crystal structure of the murine class I major histocompatibility complex H-2DB in complex with lcmv-derived…”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best…
- PDB
- 7P0T
- Type
- protein
- Length
- 721 residues
- Chains
- 6
- 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; Derived…
- UniProt
- P01899, P01887
- Ligands
- SO4, CL
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 247 | 26% helix, 38% strand | P01899 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 48% strand | P01887 |
| C, F | Derived peptide GP33-41 from lcmv | protein | 9 | 0% helix, 0% strand | — |
| D | H-2 class I histocompatibility antigen, D-B alpha chain | protein | 258 | 22% helix, 39% strand | P01899 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 635 | 0.66 | 0.76 | 65 | SO4 |
| 2 | 538 | 0.63 | 0.75 | 49 | empty |
| 3 | 100 | 0.51 | 0.82 | 24 | empty |
| 4 | 166 | 0.51 | 0.78 | 22 | empty |
| 5 | 162 | 0.49 | 0.77 | 29 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1298 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1248 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 937 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 910 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 428 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 d-amino (disulfide, D-amino acid).
Compared structures
- 7P0T · CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX… · the same entry in another collection · chain F against F, TM-score 1.00
- P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 7P0T · PDBe 7P0T · UniProt P01899 · UniProt P01887
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