MolNFT v1 · #172082 · protein
Structure of the PMT3-mir domain with bound ligands
6ZQQ · PMT3 isoform 1: “Structure of the PMT3-mir domain with bound ligands”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #172082 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZQQ
- Type
- protein
- Length
- 806 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PMT3 isoform 1
- UniProt
- A0A6A5Q4I2
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | PMT3 isoform 1 | protein | 202 | 6% helix, 42% strand | A0A6A5Q4I2 |
| D | PMT3 isoform 1 | protein | 200 | 6% helix, 44% strand | A0A6A5Q4I2 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.82 | 0.86 | 100 | GOL |
| 2 | 390 | 0.70 | 0.82 | 32 | empty |
| 3 | 204 | 0.62 | 0.82 | 32 | GOL |
| 4 | 58 | 0.41 | 0.82 | 13 | empty |
| 5 | 64 | 0.38 | 0.79 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 541 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 517 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 256 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZQQ · Structure of the Pmt3-MIR domain with bound ligands · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A6A5Q4I2
- Elsewhere: RCSB PDB 6ZQQ · PDBe 6ZQQ · UniProt A0A6A5Q4I2
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