MolNFT v1 · #136719 · protein
Crystal structure of streptococcus suis suib bound to S- adenosylmethionine
5V1S · Radical SAM: “Crystal structure of streptococcus suis suib bound to S- adenosylmethionine”. X-ray diffraction, 2 ligands (SF4, SAM), 8 pockets (best druggability 0.82). MolNFT v1 #136719 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5V1S
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radical SAM
- UniProt
- A0A0Z8EWX1
- Ligands
- SF4, SAM
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical SAM | protein | 425 | 39% helix, 15% strand | A0A0Z8EWX1 |
| B | Radical SAM | protein | 427 | 41% helix, 15% strand | A0A0Z8EWX1 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.82 | 0.83 | 88 | SF4, SAM |
| 2 | 1034 | 0.82 | 0.83 | 88 | SF4, SAM |
| 3 | 68 | 0.58 | 0.89 | 20 | SF4 |
| 4 | 460 | 0.56 | 0.73 | 50 | empty |
| 5 | 84 | 0.54 | 0.85 | 23 | SF4 |
Interfaces
1 interface between chains.
- A–B · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V1S · Crystal structure of Streptococcus suis SuiB bound to S-adenosylmethionine · the same entry in another collection · 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 A0A0Z8EWX1
- Elsewhere: RCSB PDB 5V1S · PDBe 5V1S · UniProt A0A0Z8EWX1
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