Research workbench
Crystal structure of pan-RPT5C chimera
Analyse Crystal structure of pan-RPT5C chimera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WHK
- Type
- protein
- Length
- 1,964 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
- UniProt
- Q8U4H3, P33297
- Ligands
- ATP
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 248 | 48% helix, 14% strand | Q8U4H3, P33297 |
| B, F | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 244 | 48% helix, 14% strand | Q8U4H3, P33297 |
| C, G | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 245 | 49% helix, 14% strand | Q8U4H3, P33297 |
| D | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 245 | 49% helix, 14% strand | Q8U4H3, P33297 |
| E | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 247 | 49% helix, 14% strand | Q8U4H3, P33297 |
| H | Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A | protein | 246 | 48% helix, 14% strand | Q8U4H3, P33297 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.70 | 0.75 | 123 | ATP |
| 2 | 591 | 0.67 | 0.77 | 78 | ATP |
| 3 | 493 | 0.64 | 0.77 | 63 | empty |
| 4 | 419 | 0.63 | 0.77 | 49 | empty |
| 5 | 254 | 0.58 | 0.78 | 25 | empty |
Interfaces
11 interfaces between chains.
- C–D · 1019 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 990 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 976 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 971 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 287 Ų buried · 6 hydrogen bonds · protein-protein
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 Q8U4H3
- Every structure of UniProt P33297
- Elsewhere: RCSB PDB 3WHK · PDBe 3WHK · UniProt Q8U4H3 · UniProt P33297
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