MolNFT v2 · #116955 · protein
Yeast 20S proteasome in complex with alkyne-PI
5DKI: “Yeast 20S proteasome in complex with alkyne-PI”. X-ray diffraction at 2.8, 3 ligands (5BZ, MG, CL). MolNFT v2 #116955 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DKI
- Type
- protein
- Length
- 6,344 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- UniProt
- P23639, P23638, P40303, P32379, P40302, P21242, P21243, P25043, P25451, P22141, P30656, P23724, P30657, P38624
- Ligands
- 5BZ, MG, CL
Structure
x-ray diffraction · resolution 2.8 · 14 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | — | protein | 250 | — | P23639 |
| B, P | — | protein | 244 | — | P23638 |
| C, Q | — | protein | 240 | — | P40303 |
| D, R | — | protein | 235 | — | P32379 |
| E, S | — | protein | 231 | — | P40302 |
| F, T | — | protein | 243 | — | P21242 |
| G, U | — | protein | 241 | — | P21243 |
| H, V | — | protein | 226 | — | P25043 |
| I, W | — | protein | 204 | — | P25451 |
| J, X | — | protein | 195 | — | P22141 |
| K, Y | — | protein | 212 | — | P30656 |
| L, Z | — | protein | 222 | — | P23724 |
| M, a | — | protein | 233 | — | P30657 |
| N, b | — | protein | 196 | — | P38624 |
Ligands and binding sites
- 5BZ · [(1~{R})-1-[[(2~{S})-2-(hex-5-ynoylamino)-3-phenyl-propanoyl]amino]-3-methyl-butyl]boronic acid · ligand · 6 copies · chains H, I, K, L, N, V, W, Y, b
- MG · Magnesium ion · metal · 8 copies · chains G, I, Y, J, K, W, L, V, N, a, Z
- CL · Chloride ion · ion · 5 copies · chains G, H, N, U, V, b
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5DKI · Yeast 20S proteasome in complex with alkyne-pi · 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 5DKI · PDBe 5DKI · 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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