Research workbench
Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant, refined at 1.60 ångströms resolution
Analyse Model of MHC class ib H2-M3 with mouse ND1 N-terminal heptapeptide, thr mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LFK
- Type
- protein
- Length
- 762 residues
- Chains
- 6
- 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, NA
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histocompatibility 2, M region locus 3 | protein | 275 | 28% helix, 40% strand | Q31093 |
| B, E | Beta-2-microglobulin | protein | 99 | 0% helix, 52% strand | P01887 |
| C, F | 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
- NA · Sodium ion · metal · 6 copies · chains A, D, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.68 | 0.79 | 44 | empty |
| 2 | 601 | 0.66 | 0.77 | 52 | empty |
| 3 | 412 | 0.64 | 0.78 | 57 | empty |
| 4 | 185 | 0.58 | 0.81 | 25 | empty |
| 5 | 237 | 0.57 | 0.79 | 36 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1401 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1292 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 852 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 833 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 812 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified, 1 glycan (disulfide, formylation, N-glycosylation).
Compared structures
- 7LFK · MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, THR MUTANT, REFINED… · 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 0.99
- 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 0.51
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 7LFK · PDBe 7LFK · UniProt Q31093 · UniProt P01887 · UniProt P03888
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