MolNFT v1 · #74703 · protein
Crystal structure of H2-kb in complex with the NP205-lcmv epitope ytvkypnl, an 8-mer peptide from the lcmv
3P4M · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H2-kb in complex with the NP205-lcmv epitope ytvkypnl, an 8-mer peptide from the lcmv”. X-ray diffraction, 1 ligand (ACE), 11 pockets (best druggability…
- PDB
- 3P4M
- Type
- protein
- Length
- 769 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; NP205-lcmv…
- UniProt
- P01901, P01887, Q91B91
- Ligands
- ACE
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 278 | 25% helix, 38% strand | P01901 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P01887 |
| C, F | NP205-lcmv epitope, ytvkypnl | protein | 8 | 0% helix, 0% strand | Q91B91 |
| D | H-2 class I histocompatibility antigen, K-B alpha chain | protein | 277 | 26% helix, 39% strand | P01901 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.63 | 0.74 | 60 | ACE |
| 2 | 585 | 0.61 | 0.74 | 57 | ACE |
| 3 | 167 | 0.52 | 0.79 | 28 | empty |
| 4 | 97 | 0.45 | 0.80 | 19 | empty |
| 5 | 164 | 0.45 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1234 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1188 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 927 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 920 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 662 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3P4M · Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer… · 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 0.99
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 Q91B91
- Elsewhere: RCSB PDB 3P4M · PDBe 3P4M · UniProt P01901 · UniProt P01887 · UniProt Q91B91
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