Research workbench
Structure and function based design of plasmodium-selective proteasome inhibitors
Analyse Structure and function based design of plasmodium-selective proteasome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FMG
- Type
- protein
- Length
- 5,716 residues
- Chains
- 28
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasome subunit alpha, putative; Proteasome subunit alpha type 2, putative; Proteasome…
- EC
- 3.4.25.1
- UniProt
- Q8IAR3, C6KST3, Q8IDG3, Q8IDG2, Q8IBI3, Q8IK90, O77396, Q8I0U7, Q8I6T3, Q8I261, Q8IKC9, Q8IJT1, C0H4E8, Q7K6A9
- Ligands
- 7F1
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 14 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, O | Proteasome subunit alpha, putative (EC 3.4.25.1) | protein | 219 | 33% helix, 13% strand | Q8IAR3 |
| B, P | Proteasome subunit alpha type 2, putative (EC 3.4.25.1) | protein | 212 | 37% helix, 13% strand | C6KST3 |
| C, Q | Proteasome subunit alpha type (EC 3.4.25.1) | protein | 220 | 40% helix, 15% strand | Q8IDG3 |
| D, R | Proteasome subunit alpha type (EC 3.4.25.1) | protein | 215 | 37% helix, 24% strand | Q8IDG2 |
| E, S | Proteasome subunit alpha type (EC 3.4.25.1) | protein | 217 | 34% helix, 17% strand | Q8IBI3 |
| F, T | Proteosome subunit alpha type 1, putative | protein | 219 | 34% helix, 16% strand | Q8IK90 |
| G, U | Proteasome component C8, putative | protein | 219 | 35% helix, 17% strand | O77396 |
| H, V | Proteasome, putative (EC 3.4.25.1) | protein | 191 | 30% helix, 24% strand | Q8I0U7 |
| I, W | Proteasome subunit beta type (EC 3.4.25.1) | protein | 186 | 33% helix, 28% strand | Q8I6T3 |
| J, X | BETA3 proteasome subunit, putative (EC 3.4.25.1) | protein | 191 | 32% helix, 24% strand | Q8I261 |
| K, Y | Proteasome subunit beta type (EC 3.4.25.1) | protein | 194 | 29% helix, 24% strand | Q8IKC9 |
| L, Z | Proteasome subunit beta type (EC 3.4.25.1) | protein | 189 | 32% helix, 24% strand | Q8IJT1 |
| M, a | Proteasome subunit beta type (EC 3.4.25.1) | protein | 199 | 31% helix, 22% strand | C0H4E8 |
| N, b | Proteasome subunit beta type (EC 3.4.25.1) | protein | 187 | 33% helix, 32% strand | Q7K6A9 |
Ligands and binding sites
- 7F1 · (2S)-N-[(E,2S)-1-(1H-indol-3-yl)-4-methylsulfonyl-but-3-en-2-yl]-2-[[(2S)-3-(1H-indol-3-yl)-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]-4-methyl-pentanamide · ligand · 2 copies · chains I, J, W, X
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 | 897 | 0.77 | 0.80 | 94 | empty |
| 2 | 1017 | 0.77 | 0.79 | 119 | empty |
| 3 | 1148 | 0.75 | 0.78 | 116 | empty |
| 4 | 895 | 0.74 | 0.78 | 93 | empty |
| 5 | 1163 | 0.74 | 0.77 | 123 | empty |
Interfaces
70 interfaces between chains.
- A–G · 1010 Ų buried · 5 hydrogen bonds · protein-protein
- Q–R · 1005 Ų buried · 12 hydrogen bonds · protein-protein
- O–U · 1004 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 967 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 5FMG · Structure and function based design of Plasmodium-selective proteasome inhibitors · the same entry in another collection · chain T against T, 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 Q8IAR3
- Every structure of UniProt C6KST3
- Every structure of UniProt Q8IDG3
- Every structure of UniProt Q8IDG2
- Every structure of UniProt Q8IBI3
- Every structure of UniProt Q8IK90
- Every structure of UniProt O77396
- Every structure of UniProt Q8I0U7
- Every structure of UniProt Q8I6T3
- Every structure of UniProt Q8I261
- Every structure of UniProt Q8IKC9
- Every structure of UniProt Q8IJT1
- Every structure of UniProt C0H4E8
- Every structure of UniProt Q7K6A9
- Elsewhere: RCSB PDB 5FMG · PDBe 5FMG · UniProt Q8IAR3 · UniProt C6KST3 · UniProt Q8IDG3 · UniProt Q8IDG2 · UniProt Q8IBI3 · UniProt Q8IK90 · UniProt O77396 · UniProt Q8I0U7 · UniProt Q8I6T3 · UniProt Q8I261 · UniProt Q8IKC9 · UniProt Q8IJT1 · UniProt C0H4E8 · UniProt Q7K6A9
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