Research workbench
Murine class I major histocompatibility complex H-2KB in complex with immunodominant lcmv-derived GP34-41 peptide
Analyse Murine class I major histocompatibility complex H-2KB in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ROO
- Type
- protein
- Length
- 760 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Murine class I major histocompatibility complex H-2KB; Beta-2-microglobulin…
- UniProt
- P01887, Q9QDK7
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Murine class I major histocompatibility complex H-2KB | protein | 275 | 28% helix, 39% strand | — |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 53% strand | P01887 |
| C | Murine class I major histocompatibility complex H-2KB | protein | 271 | 28% helix, 39% strand | — |
| E, F | Pre-glycoprotein polyprotein gp complex | protein | 8 | 0% helix, 0% strand | Q9QDK7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.73 | 0.76 | 99 | empty |
| 2 | 247 | 0.61 | 0.80 | 37 | GOL, MPD, PO4 |
| 3 | 248 | 0.58 | 0.79 | 42 | MPD, PO4, GOL |
| 4 | 63 | 0.53 | 0.87 | 18 | empty |
| 5 | 137 | 0.51 | 0.80 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1390 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1279 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 863 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 850 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3ROO · Murine class I major histocompatibility complex H-2Kb in complex with immunodominant… · 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 D against A, TM-score 0.97
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 P01887
- Every structure of UniProt Q9QDK7
- Elsewhere: RCSB PDB 3ROO · PDBe 3ROO · UniProt P01887 · UniProt Q9QDK7
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