Research workbench
Crystal structure of yeast 20S proteasome in complex with the natural product carmaphycin a
Analyse Crystal structure of yeast 20S proteasome in complex with the natural product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HRD
- Type
- protein
- Length
- 6,368 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome component Y7; Proteasome component Y13; Proteasome component PRE6; Proteasome…
- EC
- 3.4.25.1
- UniProt
- P23639, P23638, P40303, P32379, P40302, P21242, P21243, P25043, P25451, P22141, P30656, P23724, P30657, P38624
- Ligands
- OV1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 14 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome component Y7 (EC 3.4.25.1) | protein | 250 | 36% helix, 26% strand | P23639 |
| B, P | Proteasome component Y13 (EC 3.4.25.1) | protein | 244 | 38% helix, 26% strand | P23638 |
| C, Q | Proteasome component PRE6 (EC 3.4.25.1) | protein | 241 | 34% helix, 24% strand | P40303 |
| D, R | Proteasome component PUP2 (EC 3.4.25.1) | protein | 242 | 37% helix, 26% strand | P32379 |
| E, S | Proteasome component PRE5 (EC 3.4.25.1) | protein | 233 | 36% helix, 25% strand | P40302 |
| F, T | Proteasome component C1 (EC 3.4.25.1) | protein | 244 | 38% helix, 26% strand | P21242 |
| G, U | Proteasome component C7-alpha (EC 3.4.25.1) | protein | 243 | 40% helix, 23% strand | P21243 |
| H, V | Proteasome component PUP1 (EC 3.4.25.1) | protein | 222 | 29% helix, 36% strand | P25043 |
| I, W | Proteasome component PUP3 (EC 3.4.25.1) | protein | 204 | 32% helix, 33% strand | P25451 |
| J, X | Proteasome component C11 (EC 3.4.25.1) | protein | 198 | 34% helix, 34% strand | P22141 |
| K, Y | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 35% helix, 35% strand | P30656 |
| L, Z | Proteasome component C5 (EC 3.4.25.1) | protein | 222 | 28% helix, 32% strand | P23724 |
| M, a | Proteasome component PRE4 (EC 3.4.25.1) | protein | 233 | 30% helix, 31% strand | P30657 |
| N, b | Proteasome component PRE3 (EC 3.4.25.1) | protein | 196 | 36% helix, 35% strand | P38624 |
Ligands and binding sites
- OV1 · N-[(2S)-1-({(2S)-1-{[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]amino}-4-[(R)-methylsulfinyl]-1-oxobutan-2-yl}amino)-3-methyl-1-oxobutan-2-yl]hexanamide · ligand · 6 copies · chains H, I, Z, K, L, N, V, W, Y, b
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 | 968 | 0.83 | 0.84 | 118 | empty |
| 2 | 1016 | 0.83 | 0.84 | 120 | OV1 |
| 3 | 1102 | 0.80 | 0.82 | 114 | empty |
| 4 | 1189 | 0.80 | 0.81 | 111 | empty |
| 5 | 1086 | 0.80 | 0.82 | 105 | empty |
Interfaces
92 interfaces between chains.
- H–I · 1710 Ų buried · 27 hydrogen bonds · protein-protein
- V–W · 1703 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1649 Ų buried · 22 hydrogen bonds · protein-protein
- P–Q · 1612 Ų buried · 22 hydrogen bonds · protein-protein
- A–G · 1498 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4HRD · Crystal structure of yeast 20S proteasome in complex with the natural product carmaphycin… · 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 4HRD · PDBe 4HRD · 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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