MolNFT v1 · #77763 · protein
Murine class I major histocompatibility complex H-2KB in complex with post-translationally modified lcmv-derived GP34-41 peptide, comprising a nitrotyrosine at position 3
3ROL · H-2 class I histocompatibility antigen, K-B alpha chain: “Murine class I major histocompatibility complex H-2KB in complex with post-translationally modified…”. X-ray diffraction, 1 ligand (PO4), 10 pockets (best druggability 0.74).…
- PDB
- 3ROL
- Type
- protein
- Length
- 757 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…
- UniProt
- P01901, P01887, Q9QDK7
- Ligands
- PO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 271 | 28% helix, 40% strand | P01901 |
| B, D | Beta-2-microglobulin | protein | 99 | 0% helix, 55% strand | P01887 |
| C | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 272 | 28% helix, 40% strand | P01901 |
| 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 · chains C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.74 | 0.77 | 100 | empty |
| 2 | 205 | 0.57 | 0.80 | 31 | GOL, MPD, PO4 |
| 3 | 222 | 0.57 | 0.79 | 34 | PO4 |
| 4 | 62 | 0.55 | 0.88 | 18 | empty |
| 5 | 62 | 0.51 | 0.86 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1394 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 858 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 854 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 728 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 3ROL · Murine class I major histocompatibility complex H-2Kb in complex with… · 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 B 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 P01901
- Every structure of UniProt P01887
- Every structure of UniProt Q9QDK7
- Elsewhere: RCSB PDB 3ROL · PDBe 3ROL · UniProt P01901 · UniProt P01887 · UniProt Q9QDK7
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