MolNFT v1 · #11115 · protein
Crystal structure of the yeast 20S PROTEASOME:TMC-95A complex: a non- covalent proteasome inhibitor
1JD2 · Proteasome component Y7: “Crystal structure of the yeast 20S PROTEASOME:TMC-95A complex: a non- covalent proteasome inhibitor”. X-ray diffraction, 3 ligands (1QQ, AKK, MG), 20 pockets (best druggability 0.84). MolNFT v1 #11115 on…
- PDB
- 1JD2
- Type
- protein
- Length
- 6,374 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome component Y7; Proteasome component Y13; Proteasome component PRE6; Proteasome…
- EC
- 3.4.99.46
- UniProt
- P23639, P23638, P40303, P32379, P40302, P21242, P21243, P25043, P25451, P22141, P30656, P23724, P30657, P38624
- Ligands
- 1QQ, AKK, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 15 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, V | Proteasome component Y7 (EC 3.4.99.46) | protein | 250 | 36% helix, 25% strand | P23639 |
| B, W | Proteasome component Y13 (EC 3.4.99.46) | protein | 244 | 38% helix, 22% strand | P23638 |
| C, X | Proteasome component PRE6 (EC 3.4.99.46) | protein | 241 | 37% helix, 23% strand | P40303 |
| D, Y | Proteasome component PUP2 (EC 3.4.99.46) | protein | 242 | 37% helix, 24% strand | P32379 |
| E, Z | Proteasome component PRE5 (EC 3.4.99.46) | protein | 233 | 37% helix, 27% strand | P40302 |
| F, 1 | Proteasome component C1 (EC 3.4.99.46) | protein | 244 | 39% helix, 26% strand | P21242 |
| G, 2 | Proteasome component C7-alpha (EC 3.4.99.46) | protein | 243 | 40% helix, 23% strand | P21243 |
| H, O | Proteasome component PUP1 (EC 3.4.99.46) | protein | 222 | 29% helix, 35% strand | P25043 |
| I, P | Proteasome component PUP3 (EC 3.4.99.46) | protein | 204 | 32% helix, 30% strand | P25451 |
| J, Q | Proteasome component C11 (EC 3.4.99.46) | protein | 198 | 35% helix, 32% strand | P22141 |
| K, R | Proteasome component PRE2 (EC 3.4.99.46) | protein | 212 | 36% helix, 34% strand | P30656 |
| L, S | Proteasome component C5 (EC 3.4.99.46) | protein | 222 | 29% helix, 32% strand | P23724 |
| M, T | Proteasome component PRE4 (EC 3.4.99.46) | protein | 233 | 32% helix, 30% strand | P30657 |
| N, U | Proteasome component PRE3 (EC 3.4.99.46) | protein | 196 | 38% helix, 35% strand | P38624 |
| 8, 9 | Tmc-95A inhibitor | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1QQ · (3S)-3-methyl-2-oxopentanoic acid · ligand · 2 copies · chains H, I, 8, O, P, 9
- AKK · (1Z)-prop-1-en-1-amine · ligand · 2 copies · chains H, 8, O, 9
- MG · Magnesium ion · metal · 10 copies · chains D, L, A, F, G, H, S, I, N, T, K, P
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 | 1154 | 0.84 | 0.85 | 142 | AKK |
| 2 | 999 | 0.84 | 0.85 | 104 | AKK |
| 3 | 1103 | 0.81 | 0.83 | 111 | empty |
| 4 | 1137 | 0.80 | 0.82 | 112 | empty |
| 5 | 942 | 0.80 | 0.82 | 111 | empty |
Interfaces
98 interfaces between chains.
- H–I · 1720 Ų buried · 30 hydrogen bonds · protein-protein
- O–P · 1716 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1664 Ų buried · 23 hydrogen bonds · protein-protein
- W–X · 1631 Ų buried · 20 hydrogen bonds · protein-protein
- V–W · 1508 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1JD2 · Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A non-covalent Proteasome… · the same entry in another collection · chain B against B, 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 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 P21243
- 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 P38624
- Elsewhere: RCSB PDB 1JD2 · PDBe 1JD2 · UniProt P23639 · UniProt P23638 · UniProt P40303 · UniProt P32379 · UniProt P40302 · UniProt P21242 · UniProt P21243 · UniProt P25043 · UniProt P25451 · UniProt P22141 · UniProt P30656 · UniProt P23724 · UniProt P30657 · UniProt P38624
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