MolNFT v1 · #136720 · protein
Crystal structure of streptococcus suis suib bound to precursor peptide suia
5V1T · Radical SAM: “Crystal structure of streptococcus suis suib bound to precursor peptide suia”. X-ray diffraction, 3 ligands (SF4, MET, SAM), 4 pockets (best druggability 0.85). MolNFT v1 #136720 on GenesisL1: 3D structure, binding…
- PDB
- 5V1T
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Radical SAM; Suia 22MER
- UniProt
- A0A0Z8EWX1
- Ligands
- SF4, MET, SAM
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Radical SAM | protein | 439 | 40% helix, 14% strand | A0A0Z8EWX1 |
| B | Suia 22MER | protein | 13 | 69% helix, 0% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A, B
- MET · Methionine · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.85 | 0.86 | 98 | SF4, MET, SAM |
| 2 | 312 | 0.64 | 0.81 | 38 | empty |
| 3 | 63 | 0.57 | 0.89 | 22 | SF4 |
| 4 | 53 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 717 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5V1T · Crystal structure of Streptococcus suis SuiB bound to precursor peptide SuiA · 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 5V1T · PDBe 5V1T · UniProt A0A0Z8EWX1
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