Research workbench
Structure of a minimal SF3B core in complex with sudemycin D6 (form II)
Analyse Structure of a minimal SF3B core in complex with sudemycin D6 (form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B92
- Type
- protein
- Length
- 1,862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Splicing factor 3B subunit 3; Splicing factor 3B subunit 5; Splicing factor 3B subunit 1…
- UniProt
- Q15393, Q9BWJ5, O75533, Q7RTV0
- Ligands
- T2W, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Splicing factor 3B subunit 3 | protein | 862 | 11% helix, 45% strand | Q15393 |
| B | Splicing factor 3B subunit 5 | protein | 65 | 60% helix, 0% strand | Q9BWJ5 |
| C | Splicing factor 3B subunit 1 | protein | 842 | 76% helix, 0% strand | O75533 |
| D | Phd finger-like domain-containing protein 5A | protein | 93 | 13% helix, 25% strand | Q7RTV0 |
Ligands and binding sites
- T2W · [(~{Z},2~{S})-5-[[4-[(2~{E},4~{E})-3-methyl-5-[(2~{S}, 4~{R})-4,6,6-trimethyl-4-oxidanyl-oxan-2-yl]penta-2,4-dienyl]cyclohexyl]amino]-5-oxidanylidene-pent-3-en-2-yl] ~{N}-methylcarbamate · ligand · chains C, D
- ZN · Zinc ion · metal · 3 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.85 | 0.86 | 85 | empty |
| 2 | 350 | 0.79 | 0.89 | 52 | empty |
| 3 | 1095 | 0.78 | 0.80 | 93 | empty |
| 4 | 629 | 0.77 | 0.83 | 74 | empty |
| 5 | 1084 | 0.74 | 0.77 | 91 | T2W |
Interfaces
6 interfaces between chains.
- A–C · 2348 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2323 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1455 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1240 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7B92 · Structure of a minimal SF3B core in complex with sudemycin D6 (form II) · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.99
- 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 0.92
- 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 0.89
- 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 0.81
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 Q15393
- Every structure of UniProt Q9BWJ5
- Every structure of UniProt O75533
- Every structure of UniProt Q7RTV0
- Elsewhere: RCSB PDB 7B92 · PDBe 7B92 · UniProt Q15393 · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0
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