MolNFT v1 · #129350 · protein
K33-specific affimer bound to K33 diub
5OHM · Polyubiquitin-C: “K33-specific affimer bound to K33 diub”. X-ray diffraction, 13 pockets (best druggability 0.70). MolNFT v1 #129350 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OHM
- Type
- protein
- Length
- 980 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyubiquitin-C; K33-specific affimer
- UniProt
- P0CG48
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 21% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Polyubiquitin-C | protein | 74 | 20% helix, 35% strand | P0CG48 |
| E | Polyubiquitin-C | protein | 75 | 20% helix, 35% strand | P0CG48 |
| I, K | Polyubiquitin-C | protein | 73 | 21% helix, 32% strand | P0CG48 |
| D, H | K33-specific affimer | protein | 89 | 21% helix, 57% strand | — |
| L, B | K33-specific affimer | protein | 89 | 20% helix, 61% strand | — |
| F | K33-specific affimer | protein | 91 | 21% helix, 60% strand | — |
| J | K33-specific affimer | protein | 90 | 21% helix, 61% strand | — |
Ligands and binding sites
- 15P · Polyethylene glycol (N=34) · additive · 2 copies · chains E, H, K, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.97 | 12 | empty |
| 2 | 50 | 0.69 | 0.97 | 12 | empty |
| 3 | 363 | 0.62 | 0.78 | 46 | empty |
| 4 | 322 | 0.59 | 0.77 | 51 | empty |
| 5 | 460 | 0.58 | 0.74 | 56 | empty |
Interfaces
24 interfaces between chains.
- E–G · 709 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 692 Ų buried · 4 hydrogen bonds · protein-protein
- I–K · 687 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 663 Ų buried · 18 hydrogen bonds · protein-protein
- H–F · 653 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5OHM · K33-specific affimer bound to K33 diUb · 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 P0CG48
- Elsewhere: RCSB PDB 5OHM · PDBe 5OHM · UniProt P0CG48
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