MolNFT v1 · #92347 · protein
Structure of proteasome-PBA1-PBA2 complex
4G4S · Proteasome component C7-alpha: “Structure of proteasome-PBA1-PBA2 complex”. X-ray diffraction, 3 ligands (ACE, LDZ, MG), 20 pockets (best druggability 0.84). MolNFT v1 #92347 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4G4S
- Type
- protein
- Length
- 3,544 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome component C7-alpha; Proteasome component Y7; Proteasome component Y13…
- EC
- 3.4.25.1
- UniProt
- P21243, P23639, P23638, P40303, P32379, P40302, P21242, P38624, P25043, P25451, P22141, P30656, P23724, P30657, Q05778, P36040
- Ligands
- ACE, LDZ, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 16 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasome component C7-alpha (EC 3.4.25.1) | protein | 241 | 37% helix, 23% strand | P21243 |
| B | Proteasome component Y7 (EC 3.4.25.1) | protein | 246 | 37% helix, 26% strand | P23639 |
| C | Proteasome component Y13 (EC 3.4.25.1) | protein | 237 | 35% helix, 26% strand | P23638 |
| D | Proteasome component PRE6 (EC 3.4.25.1) | protein | 220 | 38% helix, 27% strand | P40303 |
| E | Proteasome component PUP2 (EC 3.4.25.1) | protein | 249 | 36% helix, 25% strand | P32379 |
| F | Proteasome component PRE5 (EC 3.4.25.1) | protein | 234 | 36% helix, 28% strand | P40302 |
| G | Proteasome component C1 (EC 3.4.25.1) | protein | 246 | 37% helix, 26% strand | P21242 |
| H | Proteasome component PRE3 (EC 3.4.25.1) | protein | 196 | 38% helix, 34% strand | P38624 |
| I | Proteasome component PUP1 (EC 3.4.25.1) | protein | 220 | 30% helix, 35% strand | P25043 |
| J | Proteasome component PUP3 (EC 3.4.25.1) | protein | 203 | 32% helix, 32% strand | P25451 |
| K | Proteasome component C11 (EC 3.4.25.1) | protein | 195 | 35% helix, 33% strand | P22141 |
| L | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 36% helix, 31% strand | P30656 |
| M | Proteasome component C5 (EC 3.4.25.1) | protein | 222 | 29% helix, 31% strand | P23724 |
| N | Proteasome component PRE4 (EC 3.4.25.1) | protein | 233 | 32% helix, 31% strand | P30657 |
| O | Proteasome chaperone 1 | protein | 200 | 33% helix, 24% strand | Q05778 |
| P | Proteasome assembly chaperone 2 | protein | 190 | 34% helix, 21% strand | P36040 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains E, F, O, P
- LDZ · N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide · ligand · chains L, M
- MG · Magnesium ion · metal · 8 copies · chains A, H, I, J, L, M, E
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 | 828 | 0.84 | 0.86 | 95 | ACE |
| 2 | 993 | 0.83 | 0.84 | 109 | empty |
| 3 | 721 | 0.80 | 0.84 | 93 | empty |
| 4 | 977 | 0.79 | 0.81 | 117 | empty |
| 5 | 527 | 0.78 | 0.85 | 76 | empty |
Interfaces
36 interfaces between chains.
- I–J · 1714 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1415 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 19 hydrogen bonds · protein-protein
- A–G · 1382 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1368 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4G4S · Structure of Proteasome-Pba1-Pba2 Complex · the same entry in another collection · chain P against P, 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 Q05778
- Every structure of UniProt P36040
- Elsewhere: RCSB PDB 4G4S · PDBe 4G4S · 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 Q05778 · UniProt P36040
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