Research workbench
26S proteasome in presence of ATP (S2)
Analyse 26S proteasome in presence of ATP (S2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MPA
- Type
- protein
- Length
- 8,674 residues
- Chains
- 34
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-1; Proteasome subunit alpha type-2; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657, P33299, P40327, P33298, P53549, P33297, Q01939
- Ligands
- ATP, ADP, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 22 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, A | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 241 | 40% helix, 22% strand | P21243 |
| b, B | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 250 | 32% helix, 26% strand | P23639 |
| c, C | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 244 | 33% helix, 21% strand | P23638 |
| d, D | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 240 | 35% helix, 23% strand | P40303 |
| e, E | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 242 | 38% helix, 22% strand | P32379 |
| f | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 231 | 36% helix, 24% strand | P40302 |
| g, G | Probable proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 243 | 36% helix, 22% strand | P21242 |
| h, 1 | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 196 | 34% helix, 33% strand | P38624 |
| i, 2 | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 226 | 28% helix, 29% strand | P25043 |
| j, 3 | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 28% helix, 29% strand | P25451 |
| k, 4 | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 195 | 33% helix, 32% strand | P22141 |
| l, 5 | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 212 | 36% helix, 30% strand | P30656 |
| m, 6 | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 222 | 31% helix, 32% strand | P23724 |
| n | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 232 | 32% helix, 31% strand | P30657 |
| F | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 233 | 33% helix, 24% strand | P40302 |
| 7 | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 229 | 30% helix, 31% strand | P30657 |
| H | 26S protease regulatory subunit 7 homolog | protein | 390 | 36% helix, 13% strand | P33299 |
| I | 26S protease regulatory subunit 4 homolog | protein | 385 | 40% helix, 15% strand | P40327 |
| K | 26S protease regulatory subunit 6B homolog | protein | 389 | 42% helix, 15% strand | P33298 |
| L | 26S protease subunit RPT4 | protein | 388 | 40% helix, 15% strand | P53549 |
| M | 26S protease regulatory subunit 6A | protein | 381 | 39% helix, 14% strand | P33297 |
| J | 26S protease regulatory subunit 8 homolog | protein | 386 | 41% helix, 15% strand | Q01939 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 5 copies · chains H, I, J, K, L, M
- ADP · Adenosine-5'-diphosphate · ligand · chains J
- MG · Magnesium ion · metal · 6 copies · chains H, I, J, K, L, M
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 | 576 | 0.80 | 0.86 | 55 | ATP, MG |
| 2 | 779 | 0.80 | 0.84 | 85 | empty |
| 3 | 684 | 0.80 | 0.85 | 68 | ATP, MG |
| 4 | 971 | 0.80 | 0.81 | 102 | empty |
| 5 | 1087 | 0.79 | 0.81 | 124 | ADP, MG |
Interfaces
117 interfaces between chains.
- L–M · 4777 Ų buried · 46 hydrogen bonds · protein-protein
- H–I · 4276 Ų buried · 30 hydrogen bonds · protein-protein
- K–J · 3120 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 2918 Ų buried · 31 hydrogen bonds · protein-protein
- H–M · 2850 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 5MPA · 26S proteasome in presence of ATP (s2) · the same entry in another collection · chain C against C, 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 P21243
- Every structure of UniProt P23639
- Every structure of UniProt P23638
- Every structure of UniProt P40303
- Every structure of UniProt P32379
- Every structure of UniProt P40302
- Every structure of UniProt P21242
- Every structure of UniProt P38624
- Every structure of UniProt P25043
- Every structure of UniProt P25451
- Every structure of UniProt P22141
- Every structure of UniProt P30656
- Every structure of UniProt P23724
- Every structure of UniProt P30657
- Every structure of UniProt P33299
- Every structure of UniProt P40327
- Every structure of UniProt P33298
- Every structure of UniProt P53549
- Every structure of UniProt P33297
- Every structure of UniProt Q01939
- Elsewhere: RCSB PDB 5MPA · PDBe 5MPA · UniProt P21243 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P38624 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P33299 · UniProt P40327 · UniProt P33298 · UniProt P53549 · UniProt P33297 · UniProt Q01939
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