Research workbench
Human 20S proteasome complex with dihydroeponemycin at 2.0 ångström
Analyse Human 20S proteasome complex with dihydroeponemycin at 2.0 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LF1
- Type
- protein
- Length
- 6,235 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha type-2; Proteasome subunit alpha type-4; Proteasome subunit…
- EC
- 3.4.25.1
- UniProt
- P25787, P25789, O14818, P28066, P25786, P25788, P60900, Q99436, P49720, P49721, P28074, P20618, P28070, P28072
- Ligands
- 6VC, MG, K, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 20 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha type-2 (EC 3.4.25.1) | protein | 230 | 35% helix, 27% strand | P25787 |
| B, P | Proteasome subunit alpha type-4 (EC 3.4.25.1) | protein | 248 | 39% helix, 27% strand | P25789 |
| C | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 237 | 39% helix, 25% strand | O14818 |
| D, R | Proteasome subunit alpha type-5 (EC 3.4.25.1) | protein | 233 | 34% helix, 26% strand | P28066 |
| E | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 234 | 37% helix, 27% strand | P25786 |
| F | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 239 | 38% helix, 27% strand | P25788 |
| G | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 244 | 41% helix, 26% strand | P60900 |
| H, V | Proteasome subunit beta type-7 (EC 3.4.25.1) | protein | 220 | 30% helix, 35% strand | Q99436 |
| I, W | Proteasome subunit beta type-3 (EC 3.4.25.1) | protein | 204 | 31% helix, 33% strand | P49720 |
| J, X | Proteasome subunit beta type-2 (EC 3.4.25.1) | protein | 196 | 33% helix, 36% strand | P49721 |
| K | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 200 | 36% helix, 36% strand | P28074 |
| L, Z | Proteasome subunit beta type-1 (EC 3.4.25.1) | protein | 213 | 31% helix, 33% strand | P20618 |
| M, a | Proteasome subunit beta type-4 (EC 3.4.25.1) | protein | 216 | 34% helix, 34% strand | P28070 |
| N | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 202 | 35% helix, 34% strand | P28072 |
| Q | Proteasome subunit alpha type-7 (EC 3.4.25.1) | protein | 239 | 38% helix, 24% strand | O14818 |
| S | Proteasome subunit alpha type-1 (EC 3.4.25.1) | protein | 238 | 37% helix, 26% strand | P25786 |
| T | Proteasome subunit alpha type-3 (EC 3.4.25.1) | protein | 240 | 38% helix, 27% strand | P25788 |
| U | Proteasome subunit alpha type-6 (EC 3.4.25.1) | protein | 238 | 39% helix, 26% strand | P60900 |
| Y | Proteasome subunit beta type-5 (EC 3.4.25.1) | protein | 201 | 35% helix, 36% strand | P28074 |
| b | Proteasome subunit beta type-6 (EC 3.4.25.1) | protein | 203 | 36% helix, 34% strand | P28072 |
Ligands and binding sites
- 6VC · ~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2, 3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide · ligand · 6 copies · chains H, I, K, L, N, V, W, Y, Z, b
- MG · Magnesium ion · metal · 10 copies · chains H, N, Z, I, Y, J, K, W, L, V, b, X
- K · Potassium ion · metal · 6 copies · chains G, L, N, U, Z, b
- CL · Chloride ion · ion · 56 copies · chains A, B, C, G, H, I, D, E, F, N, K, J, M, O, P, Q, W, U, V, R, S, b, Y, X, a
- 1PE · Pentaethylene glycol · additive · 9 copies · chains H, I, J, D, K, L, M, V, b, G, N, U, W, X, R, Y, Z, a
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 | 1125 | 0.80 | 0.81 | 153 | CL, 6VC |
| 2 | 1148 | 0.79 | 0.81 | 150 | 6VC |
| 3 | 790 | 0.79 | 0.83 | 95 | CL |
| 4 | 961 | 0.79 | 0.81 | 96 | empty |
| 5 | 679 | 0.79 | 0.83 | 73 | empty |
Interfaces
84 interfaces between chains.
- H–I · 1651 Ų buried · 32 hydrogen bonds · protein-protein
- A–G · 1601 Ų buried · 21 hydrogen bonds · protein-protein
- O–U · 1513 Ų buried · 21 hydrogen bonds · protein-protein
- P–Q · 1494 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1473 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 6 covalent (nonstandard, covalent ligand, alkylation).
Compared structures
- 5LF1 · Human 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom · the same entry in another collection · chain D against D, 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 P25787
- Every structure of UniProt P25789
- Every structure of UniProt O14818
- Every structure of UniProt P28066
- Every structure of UniProt P25786
- Every structure of UniProt P25788
- Every structure of UniProt P60900
- Every structure of UniProt Q99436
- Every structure of UniProt P49720
- Every structure of UniProt P49721
- Every structure of UniProt P28074
- Every structure of UniProt P20618
- Every structure of UniProt P28070
- Every structure of UniProt P28072
- Elsewhere: RCSB PDB 5LF1 · PDBe 5LF1 · UniProt P25787 · UniProt P25789 · UniProt O14818 · UniProt P28066 · UniProt P25786 · UniProt P25788 · UniProt P60900 · UniProt Q99436 · UniProt P49720 · UniProt P49721 · UniProt P28074 · UniProt P20618 · UniProt P28070 · UniProt P28072
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