Research workbench
Crystal structure of de novo designed MID1-cobalt
Analyse Crystal structure of de novo designed MID1-cobalt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V1D
- Type
- protein
- Length
- 384 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Computational design, MID1-cobalt
- Ligands
- CO
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Computational design, MID1-cobalt | protein | 48 | 77% helix, 0% strand | — |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 8 copies · chains A, F, B, C, E, H, D, G
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, F, B, C, E, H, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.72 | 0.86 | 41 | empty |
| 2 | 540 | 0.68 | 0.78 | 42 | 1PE |
| 3 | 387 | 0.66 | 0.79 | 24 | 1PE |
| 4 | 275 | 0.64 | 0.81 | 29 | 1PE |
| 5 | 214 | 0.63 | 0.82 | 23 | 1PE |
Interfaces
14 interfaces between chains.
- A–F · 731 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 727 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 725 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 681 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 465 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3V1D · Crystal structure of de novo designed MID1-cobalt · 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
- Elsewhere: RCSB PDB 3V1D · PDBe 3V1D
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