Research workbench
Nucleotide-driven triple-state remodeling of the aaa-ATPase channel in the activated human 26S proteasome
Analyse Nucleotide-driven triple-state remodeling of the aaa-ATPase channel in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VFR
- Type
- protein
- Length
- 12,868 residues
- Chains
- 46
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S proteasome non-ATPase regulatory subunit 1; 26S proteasome non-ATPase regulatory…
- EC
- 3.4.19.-, 3.4.25.1
- UniProt
- Q99460, O43242, O00232, O00231, Q15008, P51665, Q9UNM6, P55036, O00487, P48556, P60900, P25787, P25789, O14818, P28066, P25786, P25788, P28072, Q99436, P49720, P49721, P28074, P20618, P28070, P35998, P62191, P62195, P43686, P62333, P17980, Q13200
- Ligands
- AGS, ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 35 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | 26S proteasome non-ATPase regulatory subunit 1 | protein | 806 | 53% helix, 3% strand | Q99460 |
| V | 26S proteasome non-ATPase regulatory subunit 3 | protein | 472 | 59% helix, 1% strand | O43242 |
| W | 26S proteasome non-ATPase regulatory subunit 12 | protein | 456 | 59% helix, 1% strand | O00232 |
| X | 26S proteasome non-ATPase regulatory subunit 11 | protein | 241 | 58% helix, 4% strand | O00231 |
| Y | 26S proteasome non-ATPase regulatory subunit 6 | protein | 378 | 61% helix, 1% strand | Q15008 |
| Z | 26S proteasome non-ATPase regulatory subunit 7 | protein | 286 | 43% helix, 8% strand | P51665 |
| a | 26S proteasome non-ATPase regulatory subunit 13 | protein | 373 | 60% helix, 1% strand | Q9UNM6 |
| b | 26S proteasome non-ATPase regulatory subunit 4 | protein | 191 | 34% helix, 10% strand | P55036 |
| c | 26S proteasome non-ATPase regulatory subunit 14 (EC 3.4.19.-) | protein | 278 | 36% helix, 13% strand | O00487 |
| d | 26S proteasome non-ATPase regulatory subunit 8 | protein | 257 | 54% helix, 2% strand | P48556 |
| e | SEM1 | protein | 40 | 23% helix, 0% strand | — |
| G | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 239 | 33% helix, 23% strand | P60900 |
| H | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 230 | 36% helix, 23% strand | P25787 |
| I | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 248 | 37% helix, 15% strand | P25789 |
| J, j | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 239 | 37% helix, 15% strand | O14818 |
| K, k | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 228 | 32% helix, 16% strand | P28066 |
| L, l | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 31% helix, 21% strand | P25786 |
| M, m | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 240 | 31% helix, 23% strand | P25788 |
| N, n | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 191 | 34% helix, 30% strand | P28072 |
| O, o | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 29% helix, 30% strand | Q99436 |
| P, p | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 30% helix, 28% strand | P49720 |
| Q, q | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 199 | 31% helix, 24% strand | P49721 |
| R, r | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 35% helix, 27% strand | P28074 |
| S, s | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 29% helix, 29% strand | P20618 |
| T, t | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 215 | 32% helix, 29% strand | P28070 |
| g | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 240 | 34% helix, 24% strand | P60900 |
| h | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 232 | 36% helix, 20% strand | P25787 |
| i | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 250 | 38% helix, 15% strand | P25789 |
| A | 26S proteasome regulatory subunit 7 | protein | 342 | 31% helix, 10% strand | P35998 |
| B | 26S proteasome regulatory subunit 4 | protein | 350 | 37% helix, 11% strand | P62191 |
| C | 26S proteasome regulatory subunit 8 | protein | 363 | 39% helix, 7% strand | P62195 |
| D | 26S proteasome regulatory subunit 6B | protein | 380 | 30% helix, 10% strand | P43686 |
| E | 26S proteasome regulatory subunit 10B | protein | 375 | 40% helix, 13% strand | P62333 |
| F | 26S proteasome regulatory subunit 6A | protein | 376 | 39% helix, 14% strand | P17980 |
| f | 26S proteasome non-ATPase regulatory subunit 2 | protein | 689 | 61% helix, 0% strand | Q13200 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, C, D, E, F
- 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 | 1020 | 0.88 | 0.89 | 128 | empty |
| 2 | 635 | 0.85 | 0.89 | 73 | empty |
| 3 | 930 | 0.85 | 0.86 | 99 | empty |
| 4 | 1124 | 0.84 | 0.85 | 117 | AGS |
| 5 | 202 | 0.82 | 0.95 | 32 | empty |
Interfaces
148 interfaces between chains.
- E–F · 3795 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 3615 Ų buried · 40 hydrogen bonds · protein-protein
- Z–c · 3584 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 2631 Ų buried · 28 hydrogen bonds · protein-protein
- V–d · 2004 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VFR · Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated… · the same entry in another collection · chain e against e, 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 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 P60900
- Every structure of UniProt P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt P28072
- Every structure of UniProt Q99436
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28074
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- 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 Q13200
- Elsewhere: RCSB PDB 5VFR · PDBe 5VFR · UniProt Q99460 · UniProt O43242 · UniProt O00232 · UniProt O00231 · UniProt Q15008 · UniProt P51665 · UniProt Q9UNM6 · UniProt P55036 · UniProt O00487 · UniProt P48556 · UniProt P60900 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P28072 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070 · UniProt P35998 · UniProt P62191 · UniProt P62195 · UniProt P43686 · UniProt P62333 · UniProt P17980 · UniProt Q13200
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