Research workbench
Crystal structure of sznf from streptomyces achromogenes var. streptozoticus nrrl 2697 with a bound N(DELTA)-hydroxy-N(OMEGA)- methyl-L-arginine intermediate
Analyse Crystal structure of sznf from streptomyces achromogenes var. streptozoticus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M9R
- Type
- protein
- Length
- 910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sznf
- EC
- 1.-.-.-
- Ligands
- J9Y, FE
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 57% 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 | 454 | 57% helix, 12% strand | — |
Ligands and binding sites
- J9Y · (2S)-2-amino-5-{[(E)-amino(methylamino)methylidene](hydroxy)azaniumyl}pentanoate · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.82 | 0.87 | 46 | empty |
| 2 | 561 | 0.81 | 0.87 | 50 | empty |
| 3 | 51 | 0.69 | 0.98 | 13 | empty |
| 4 | 66 | 0.62 | 0.91 | 20 | empty |
| 5 | 214 | 0.52 | 0.77 | 30 | J9Y, FE |
Interfaces
1 interface between chains.
- A–B · 3197 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6M9R · Crystal structure of SznF from Streptomyces achromogenes var. streptozoticus NRRL 2697… · 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 6M9R · PDBe 6M9R
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