MolNFT v1 · #142239 · protein
SF3B spliceosomal complex bound to E7107
5ZYA · Splicing factor 3B subunit 5: “SF3B spliceosomal complex bound to E7107”. Electron microscopy, 3 ligands (9B0, ZN, K), 20 pockets (best druggability 0.88). MolNFT v1 #142239 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZYA
- Type
- protein
- Length
- 2,143 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3B subunit 5; Splicing factor 3B subunit 1; Phd finger-like…
- UniProt
- Q9BWJ5, O75533, Q7RTV0, Q15393
- Ligands
- 9B0, ZN, K
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Splicing factor 3B subunit 5 | protein | 66 | 55% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 809 | 68% helix, 0% strand | O75533 |
| D | Phd finger-like domain-containing protein 5A | protein | 85 | 11% helix, 22% strand | Q7RTV0 |
| A | Splicing factor 3B subunit 3 | protein | 1183 | 6% helix, 37% strand | Q15393 |
Ligands and binding sites
- 9B0 · [(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R}, 3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate · ligand · chains C, D
- ZN · Zinc ion · metal · 3 copies · chains D
- K · Potassium ion · metal · chains 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 | 1040 | 0.88 | 0.89 | 100 | empty |
| 2 | 183 | 0.81 | 0.96 | 43 | empty |
| 3 | 739 | 0.80 | 0.83 | 68 | empty |
| 4 | 773 | 0.79 | 0.83 | 77 | empty |
| 5 | 670 | 0.78 | 0.83 | 58 | empty |
Interfaces
5 interfaces between chains.
- B–A · 2081 Ų buried · 18 hydrogen bonds · protein-protein
- C–A · 1993 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1330 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 895 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 605 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ZYA · SF3b spliceosomal complex bound to E7107 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7RTV0 · AlphaFold monomer V2.0 prediction for phd finger-like domain- containing protein 5A… · a predicted model of the same protein · chain D against A, TM-score 0.92
- Q9BWJ5 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 5 (Q9BWJ5) · a predicted model of the same protein · chain B against A, TM-score 0.87
- Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain A against A, TM-score 0.83
- O75533 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 1 (O75533) · a predicted model of the same protein · chain C against A, TM-score 0.79
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 Q9BWJ5
- Every structure of UniProt O75533
- Every structure of UniProt Q7RTV0
- Every structure of UniProt Q15393
- Elsewhere: RCSB PDB 5ZYA · PDBe 5ZYA · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0 · UniProt Q15393
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