Research workbench
Crystal structure of yeast 20S proteasome in complex with vinylketone carmaphycin analogue VNK1
Analyse Crystal structure of yeast 20S proteasome in complex with vinylketone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HNP
- 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
- VNK, ONK
- 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, 25% strand | P23638 |
| C, Q | Proteasome component PRE6 (EC 3.4.25.1) | protein | 241 | 36% helix, 23% strand | P40303 |
| D, R | Proteasome component PUP2 (EC 3.4.25.1) | protein | 242 | 37% helix, 27% strand | P32379 |
| E, S | Proteasome component PRE5 (EC 3.4.25.1) | protein | 233 | 35% helix, 26% strand | P40302 |
| F, T | Proteasome component C1 (EC 3.4.25.1) | protein | 244 | 38% helix, 25% 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, 35% strand | P25043 |
| I, W | Proteasome component PUP3 (EC 3.4.25.1) | protein | 204 | 30% helix, 34% strand | P25451 |
| J, X | Proteasome component C11 (EC 3.4.25.1) | protein | 198 | 34% helix, 33% strand | P22141 |
| K, Y | Proteasome component PRE2 (EC 3.4.25.1) | protein | 212 | 36% helix, 34% 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 | 32% helix, 30% strand | P30657 |
| N, b | Proteasome component PRE3 (EC 3.4.25.1) | protein | 196 | 38% helix, 34% strand | P38624 |
Ligands and binding sites
- VNK · N-hexanoyl-L-valyl-N~1~-[(3S,4S)-3-hydroxy-2,6-dimethylheptan-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide · ligand · 4 copies · chains K, L, H, N, Y, Z, V, b
- ONK · N-hexanoyl-L-valyl-N~1~-[(3S,4S)-3-hydroxy-2,6-dimethylhept-1-en-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide · ligand · 2 copies · chains H, I, V, W
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 | 971 | 0.83 | 0.84 | 127 | ONK |
| 2 | 853 | 0.82 | 0.84 | 117 | empty |
| 3 | 1117 | 0.80 | 0.81 | 105 | empty |
| 4 | 949 | 0.80 | 0.82 | 101 | empty |
| 5 | 1086 | 0.80 | 0.81 | 97 | empty |
Interfaces
92 interfaces between chains.
- V–W · 1694 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1679 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1625 Ų buried · 21 hydrogen bonds · protein-protein
- P–Q · 1622 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 1511 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 4HNP · Crystal structure of yeast 20S proteasome in complex with vinylketone 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 4HNP · PDBe 4HNP · 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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