MolNFT v1 · #119111 · protein
Structure of the C-terminally extended domain MY4 of human myomesin (space group P65)
5FM8 · Myomesin-1: “Structure of the C-terminally extended domain MY4 of human myomesin (space group P65)”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.61). MolNFT v1 #119111 on GenesisL1: 3D structure, binding sites…
- PDB
- 5FM8
- Type
- protein
- Length
- 404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myomesin-1
- UniProt
- P52179
- Ligands
- NI
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Myomesin-1 | protein | 101 | 0% helix, 44% strand | P52179 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains B, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.61 | 0.79 | 43 | empty |
| 2 | 286 | 0.53 | 0.75 | 38 | TRS |
| 3 | 231 | 0.50 | 0.75 | 29 | empty |
Interfaces
4 interfaces between chains.
- B–D · 583 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 566 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 549 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5FM8 · Structure of the C-terminally extended domain My4 of human myomesin (space group P65) · the same entry in another collection · chain A against A, TM-score 1.00
- P52179 · AlphaFold monomer V2.0 prediction for myomesin-1 (P52179) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P52179
- Elsewhere: RCSB PDB 5FM8 · PDBe 5FM8 · UniProt P52179
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