Research workbench
Structure of the wild-type discoidin II from dictyostelium discoideum
Analyse Structure of the wild-type discoidin II from dictyostelium discoideum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VME
- Type
- protein
- Length
- 1,534 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Discoidin-2
- UniProt
- P42530
- Ligands
- CA, ZN, CL
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Discoidin-2 | protein | 256 | 4% helix, 51% strand | P42530 |
| C, F | Discoidin-2 | protein | 255 | 4% helix, 51% strand | P42530 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 15 copies · chains A, C, B, D, E, F
- PG4 · Tetraethylene glycol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.86 | 0.89 | 87 | empty |
| 2 | 488 | 0.86 | 0.93 | 54 | empty |
| 3 | 508 | 0.86 | 0.92 | 56 | empty |
| 4 | 701 | 0.86 | 0.90 | 85 | empty |
| 5 | 993 | 0.71 | 0.75 | 80 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2094 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2081 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2077 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2053 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 1974 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
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 P42530
- Elsewhere: RCSB PDB 2VME · PDBe 2VME · UniProt P42530
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