Research workbench
Conformational landscape of the P28-bound human proteasome regulatory particle
Analyse Conformational landscape of the P28-bound human proteasome regulatory particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VHI
- Type
- protein
- Length
- 6,903 residues
- Chains
- 19
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome regulatory subunit 7; 26S proteasome regulatory subunit 4; 26S proteasome…
- EC
- 3.4.19.-
- UniProt
- P35998, P62191, P62195, P43686, P62333, P17980, Q99460, O43242, O00232, O00231, Q15008, P51665, Q9UNM6, P55036, O00487, P48556, O75832, P60896, Q13200
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 19 distinct chains · 52% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 26S proteasome regulatory subunit 7 | protein | 321 | 39% helix, 10% strand | P35998 |
| B | 26S proteasome regulatory subunit 4 | protein | 298 | 36% helix, 12% strand | P62191 |
| C | 26S proteasome regulatory subunit 8 | protein | 350 | 46% helix, 11% strand | P62195 |
| D | 26S proteasome regulatory subunit 6B | protein | 343 | 45% helix, 8% strand | P43686 |
| E | 26S proteasome regulatory subunit 10B | protein | 311 | 40% helix, 11% strand | P62333 |
| F | 26S proteasome regulatory subunit 6A | protein | 351 | 40% helix, 12% strand | P17980 |
| U | 26S proteasome non-ATPase regulatory subunit 1 | protein | 845 | 53% helix, 2% strand | Q99460 |
| V | 26S proteasome non-ATPase regulatory subunit 3 | protein | 488 | 54% helix, 0% strand | O43242 |
| W | 26S proteasome non-ATPase regulatory subunit 12 | protein | 456 | 58% helix, 0% strand | O00232 |
| X | 26S proteasome non-ATPase regulatory subunit 11 | protein | 385 | 72% helix, 1% strand | O00231 |
| Y | 26S proteasome non-ATPase regulatory subunit 6 | protein | 378 | 67% helix, 2% strand | Q15008 |
| Z | 26S proteasome non-ATPase regulatory subunit 7 | protein | 286 | 44% helix, 15% strand | P51665 |
| a | 26S proteasome non-ATPase regulatory subunit 13 | protein | 374 | 63% helix, 1% strand | Q9UNM6 |
| b | 26S proteasome non-ATPase regulatory subunit 4 | protein | 191 | 33% helix, 17% strand | P55036 |
| c | 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) | protein | 287 | 40% helix, 14% strand | O00487 |
| d | 26S proteasome non-ATPase regulatory subunit 8 | protein | 257 | 56% helix, 1% strand | P48556 |
| G | 26S proteasome non-ATPase regulatory subunit 10 | protein | 226 | 50% helix, 0% strand | O75832 |
| e | 26S proteasome complex subunit SEM1 | protein | 70 | 59% helix, 0% strand | P60896 |
| f | 26S proteasome non-ATPase regulatory subunit 2 | protein | 686 | 63% helix, 0% strand | Q13200 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains c
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.89 | 0.91 | 149 | empty |
| 2 | 1064 | 0.89 | 0.90 | 143 | empty |
| 3 | 918 | 0.87 | 0.89 | 116 | empty |
| 4 | 917 | 0.85 | 0.86 | 108 | empty |
| 5 | 978 | 0.84 | 0.85 | 110 | empty |
Interfaces
60 interfaces between chains.
- C–D · 3614 Ų buried · 36 hydrogen bonds · protein-protein
- Z–c · 3457 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 2886 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2085 Ų buried · 20 hydrogen bonds · protein-protein
- V–d · 2001 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 5VHI · Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle · the same entry in another collection · chain X against X, 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 P35998
- Every structure of UniProt P62191
- Every structure of UniProt P62195
- Every structure of UniProt P43686
- Every structure of UniProt P62333
- Every structure of UniProt P17980
- Every structure of UniProt Q99460
- Every structure of UniProt O43242
- Every structure of UniProt O00232
- Every structure of UniProt O00231
- Every structure of UniProt Q15008
- Every structure of UniProt P51665
- Every structure of UniProt Q9UNM6
- Every structure of UniProt P55036
- Every structure of UniProt O00487
- Every structure of UniProt P48556
- Every structure of UniProt O75832
- Every structure of UniProt P60896
- Every structure of UniProt Q13200
- Elsewhere: RCSB PDB 5VHI · PDBe 5VHI · UniProt P35998 · UniProt P62191 · UniProt P62195 · UniProt P43686 · UniProt P62333 · UniProt P17980 · UniProt Q99460 · UniProt O43242 · UniProt O00232 · UniProt O00231 · UniProt Q15008 · UniProt P51665 · UniProt Q9UNM6 · UniProt P55036 · UniProt O00487 · UniProt P48556 · UniProt O75832 · UniProt P60896 · UniProt Q13200
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