Research workbench
Pwwp domain of human mutated melanoma-associated antigen 1
Analyse Pwwp domain of human mutated melanoma-associated antigen 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PMI
- Type
- protein
- Length
- 485 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pwwp domain-containing protein MUM1
- UniProt
- Q2TAK8
- Ligands
- UNL, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pwwp domain-containing protein MUM1 | protein | 122 | 40% helix, 20% strand | Q2TAK8 |
| C | Pwwp domain-containing protein MUM1 | protein | 121 | 42% helix, 21% strand | Q2TAK8 |
| D | Pwwp domain-containing protein MUM1 | protein | 120 | 46% helix, 21% strand | Q2TAK8 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.79 | 0.80 | 61 | PEG |
| 2 | 252 | 0.66 | 0.83 | 36 | empty |
| 3 | 278 | 0.49 | 0.73 | 33 | empty |
| 4 | 69 | 0.32 | 0.74 | 13 | empty |
| 5 | 61 | 0.31 | 0.75 | 9 | UNL |
Interfaces
4 interfaces between chains.
- A–D · 534 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 532 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 152 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 73 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 3PMI · PWWP Domain of Human Mutated Melanoma-Associated Antigen 1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q2TAK8 · AlphaFold monomer V2.0 prediction for pwwp domain-containing DNA repair factor 3A (Q2TAK8) · a predicted model of the same protein · chain D 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 Q2TAK8
- Elsewhere: RCSB PDB 3PMI · PDBe 3PMI · UniProt Q2TAK8
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