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
- 5VFO
- Type
- protein
- Length
- 6,215 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-6; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P60900, P25787, P25789, O14818, P28066, P25786, P25788, P28072, Q99436, P49720, P49721, P28074, P20618, P28070
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 17 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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, 24% strand | P25787 |
| I | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 248 | 38% helix, 15% strand | P25789 |
| J, j | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 239 | 37% helix, 16% strand | O14818 |
| K, k | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 228 | 31% helix, 18% strand | P28066 |
| L, l | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 32% helix, 21% strand | P25786 |
| M, m | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 240 | 31% helix, 22% strand | P25788 |
| N, n | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 191 | 33% helix, 30% strand | P28072 |
| O, o | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 29% helix, 28% strand | Q99436 |
| P, p | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 31% helix, 29% strand | P49720 |
| Q, q | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 199 | 31% helix, 23% strand | P49721 |
| R, r | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 36% helix, 26% 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 | 34% helix, 30% strand | P28070 |
| g | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 240 | 35% helix, 21% strand | P60900 |
| h | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 232 | 36% helix, 21% strand | P25787 |
| i | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 250 | 38% helix, 14% strand | P25789 |
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 | 1090 | 0.79 | 0.80 | 115 | empty |
| 2 | 1108 | 0.79 | 0.80 | 107 | empty |
| 3 | 1022 | 0.79 | 0.80 | 108 | empty |
| 4 | 1095 | 0.78 | 0.80 | 116 | empty |
| 5 | 846 | 0.78 | 0.81 | 84 | empty |
Interfaces
77 interfaces between chains.
- o–p · 1564 Ų buried · 21 hydrogen bonds · protein-protein
- O–P · 1555 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 1430 Ų buried · 19 hydrogen bonds · protein-protein
- h–i · 1393 Ų buried · 15 hydrogen bonds · protein-protein
- G–M · 1383 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5VFO · Nucleotide-driven Triple-state Remodeling of the AAA-ATPase Channel in the Activated… · the same entry in another collection · chain Q against Q, 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 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
- Elsewhere: RCSB PDB 5VFO · PDBe 5VFO · 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
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