Research workbench
Structure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus with zinc occupied midas motif
Analyse Structure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CN9
- Type
- protein
- Length
- 793 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proximal thread matrix protein 1
- UniProt
- Q8T5C2
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proximal thread matrix protein 1 | protein | 397 | 38% helix, 26% strand | Q8T5C2 |
| B | Proximal thread matrix protein 1 | protein | 396 | 39% helix, 26% strand | Q8T5C2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.63 | 0.78 | 45 | empty |
| 2 | 256 | 0.57 | 0.78 | 23 | empty |
| 3 | 165 | 0.47 | 0.76 | 23 | empty |
| 4 | 192 | 0.43 | 0.73 | 37 | GOL |
| 5 | 76 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 155 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4CN9 · structure of proximal thread matrix protein 1 (PTMP1) from the mussel byssus with zinc… · 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 Q8T5C2
- Elsewhere: RCSB PDB 4CN9 · PDBe 4CN9 · UniProt Q8T5C2
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