Research workbench
Crystal structure of semet sznf from streptomyces achromogenes var. streptozoticus nrrl 2697
Analyse Crystal structure of semet sznf from streptomyces achromogenes var.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M9S
- Type
- protein
- Length
- 1,821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sznf
- EC
- 1.-.-.-
- Ligands
- FE, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sznf (EC 1.-.-.-) | protein | 456 | 56% helix, 12% strand | — |
| B | Sznf (EC 1.-.-.-) | protein | 449 | 56% helix, 12% strand | — |
| C | Sznf (EC 1.-.-.-) | protein | 459 | 56% helix, 12% strand | — |
| D | Sznf (EC 1.-.-.-) | protein | 457 | 55% helix, 12% strand | — |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.81 | 0.87 | 51 | empty |
| 2 | 602 | 0.81 | 0.86 | 53 | empty |
| 3 | 598 | 0.80 | 0.85 | 50 | empty |
| 4 | 664 | 0.80 | 0.85 | 55 | empty |
| 5 | 79 | 0.74 | 0.97 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3309 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3056 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 155 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 147 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 6M9S · Crystal structure of SeMet SznF from Streptomyces achromogenes var. streptozoticus NRRL… · 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
- Elsewhere: RCSB PDB 6M9S · PDBe 6M9S
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