Research workbench
K6-specific affimer bound to K6 diub
Analyse K6-specific affimer bound to K6 diub in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OHL
- Type
- protein
- Length
- 1,304 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- K6-specific affimer; Polyubiquitin-B
- UniProt
- P0CG47
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H | K6-specific affimer | protein | 89 | 21% helix, 58% strand | — |
| F | K6-specific affimer | protein | 88 | 22% helix, 59% strand | — |
| I, K, M | Polyubiquitin-B | protein | 75 | 24% helix, 35% strand | P0CG47 |
| J, P | Polyubiquitin-B | protein | 73 | 25% helix, 34% strand | P0CG47 |
| L, N, O | Polyubiquitin-B | protein | 74 | 24% helix, 35% strand | P0CG47 |
Ligands and binding sites
- 15P · Polyethylene glycol (N=34) · additive · 4 copies · chains A, B, C, E, D, F, G, H
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.70 | 0.79 | 59 | 15P |
| 2 | 744 | 0.69 | 0.76 | 73 | empty |
| 3 | 330 | 0.65 | 0.80 | 29 | 15P |
| 4 | 242 | 0.62 | 0.81 | 24 | empty |
| 5 | 243 | 0.59 | 0.80 | 26 | empty |
Interfaces
36 interfaces between chains.
- A–C · 2346 Ų buried · 35 hydrogen bonds · protein-protein
- F–G · 2333 Ų buried · 29 hydrogen bonds · protein-protein
- D–H · 2300 Ų buried · 32 hydrogen bonds · protein-protein
- B–E · 2281 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5OHL · K6-specific affimer bound to K6 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 P0CG47
- Elsewhere: RCSB PDB 5OHL · PDBe 5OHL · UniProt P0CG47
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