MolNFT v1 · #180940 · protein
Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant, monoclinic cell, refined at 1.60 ångströms resolution
7LFL · Histocompatibility 2, M region locus 3: “Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, val mutant, monoclinic cell, refined at…”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 7LFL
- Type
- protein
- Length
- 379 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histocompatibility 2, M region locus 3; Beta-2-microglobulin; Heptapeptide from…
- EC
- 7.1.1.2
- UniProt
- Q31093, P01887, P03888
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histocompatibility 2, M region locus 3 | protein | 275 | 28% helix, 40% strand | Q31093 |
| B | Beta-2-microglobulin | protein | 97 | 0% helix, 48% strand | P01887 |
| C | Heptapeptide from NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2) | protein | 7 | 0% helix, 0% strand | P03888 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.68 | 0.77 | 58 | empty |
| 2 | 194 | 0.55 | 0.79 | 34 | empty |
| 3 | 50 | 0.38 | 0.81 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1237 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 815 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, formylation).
Compared structures
- 7LFL · MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, VAL MUTANT… · the same entry in another collection · chain A against A, 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
- P03888 · AlphaFold monomer V2.0 prediction for NADH-ubiquinone oxidoreductase chain 1 (P03888) · a predicted model of the same protein · chain C against A, TM-score 0.42
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 Q31093
- Every structure of UniProt P01887
- Every structure of UniProt P03888
- Elsewhere: RCSB PDB 7LFL · PDBe 7LFL · UniProt Q31093 · UniProt P01887 · UniProt P03888
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