MolNFT v1 · #147792 · protein
Structure of the human plc editing module
6ENY · Beta-2-microglobulin: “Structure of the human plc editing module”. Electron microscopy, 3 ligands (MAN, NAG, BGC), 20 pockets (best druggability 0.84). MolNFT v1 #147792 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ENY
- Type
- protein
- Length
- 1,563 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-2-microglobulin; Tapasin; Protein disulfide-isomerase A3; HLA class I…
- EC
- 5.3.4.1
- UniProt
- P61769, O15533, P30101, P04439, P27797
- Ligands
- MAN, NAG, BGC
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Beta-2-microglobulin | protein | 99 | 0% helix, 39% strand | P61769 |
| C | Tapasin | protein | 364 | 5% helix, 38% strand | O15533 |
| D | Protein disulfide-isomerase A3 (EC 5.3.4.1) | protein | 461 | 31% helix, 21% strand | P30101 |
| F | HLA class I histocompatibility antigen, a-3 alpha chain | protein | 274 | 25% helix, 40% strand | P04439 |
| G | Calreticulin | protein | 365 | 17% helix, 30% strand | P27797 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F, G
- BGC · beta-D-glucopyranose · sugar · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.84 | 0.85 | 165 | empty |
| 2 | 1121 | 0.83 | 0.85 | 130 | empty |
| 3 | 974 | 0.81 | 0.83 | 121 | empty |
| 4 | 613 | 0.74 | 0.82 | 78 | empty |
| 5 | 494 | 0.72 | 0.82 | 89 | empty |
Interfaces
7 interfaces between chains.
- C–D · 486 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 452 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 235 Ų buried · 1 hydrogen bond · protein-protein
- D–G · 180 Ų buried · 1 hydrogen bond · protein-protein
- C–G · 166 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 6ENY · Structure of the human PLC editing module · the same entry in another collection · chain G against G, TM-score 1.00
- P04439 · AlphaFold monomer V2.0 prediction for HLA class I histocompatibility antigen, a alpha… · a predicted model of the same protein · chain F against A, TM-score 0.98
- P30101 · AlphaFold monomer V2.0 prediction for protein disulfide-isomerase A3 (P30101) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P27797 · AlphaFold monomer V2.0 prediction for calreticulin (P27797) · a predicted model of the same protein · chain G against A, TM-score 0.94
- O15533 · AlphaFold monomer V2.0 prediction for tapasin (O15533) · a predicted model of the same protein · chain C against A, TM-score 0.90
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P61769
- Every structure of UniProt O15533
- Every structure of UniProt P30101
- Every structure of UniProt P04439
- Every structure of UniProt P27797
- Elsewhere: RCSB PDB 6ENY · PDBe 6ENY · UniProt P61769 · UniProt O15533 · UniProt P30101 · UniProt P04439 · UniProt P27797
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