MolNFT v1 · #83429 · protein
Crystal structure of the SLD3/TRESLIN domain from yeast SLD3
3WI3 · DNA replication regulator SLD3: “Crystal structure of the SLD3/TRESLIN domain from yeast SLD3”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.67). MolNFT v1 #83429 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3WI3
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA replication regulator SLD3
- UniProt
- P53135
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA replication regulator SLD3 | protein | 215 | 72% helix, 0% strand | P53135 |
| B | DNA replication regulator SLD3 | protein | 212 | 76% helix, 0% strand | P53135 |
| C | DNA replication regulator SLD3 | protein | 205 | 72% helix, 0% strand | P53135 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.67 | 0.87 | 23 | empty |
| 2 | 143 | 0.65 | 0.87 | 31 | EDO |
| 3 | 371 | 0.63 | 0.78 | 35 | EDO |
| 4 | 80 | 0.52 | 0.85 | 15 | EDO |
| 5 | 85 | 0.52 | 0.84 | 15 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 660 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 601 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3WI3 · Crystal Structure of the Sld3/Treslin domain from yeast Sld3 · the same entry in another collection · chain A against A, TM-score 1.00
- P53135 · AlphaFold monomer V2.0 prediction for DNA replication regulator SLD3 (P53135) · a predicted model of the same protein · chain A against A, 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 P53135
- Elsewhere: RCSB PDB 3WI3 · PDBe 3WI3 · UniProt P53135
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