MolNFT v1 · #118091 · protein
Crystal structure of the epimerase snon in complex with NI2+, succinate and nogalamycin ro
5ERL · SNON,SNON: “Crystal structure of the epimerase snon in complex with NI2+, succinate and nogalamycin ro”. X-ray diffraction, 2 ligands (5R6, NI), 11 pockets (best druggability 0.80). MolNFT v1 #118091 on GenesisL1: 3D structure…
- PDB
- 5ERL
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SNON,SNON
- UniProt
- Q9RN67, Q9EYI0
- Ligands
- 5R6, NI
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SNON,SNON | protein | 257 | 28% helix, 27% strand | Q9RN67, Q9EYI0 |
| B | SNON,SNON | protein | 256 | 28% helix, 27% strand | Q9RN67, Q9EYI0 |
| D | SNON,SNON | protein | 258 | 28% helix, 26% strand | Q9RN67, Q9EYI0 |
Ligands and binding sites
- 5R6 · Nogalamycin RO · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.80 | 0.89 | 51 | empty |
| 2 | 662 | 0.80 | 0.85 | 79 | empty |
| 3 | 971 | 0.78 | 0.80 | 83 | empty |
| 4 | 309 | 0.75 | 0.87 | 37 | SIN, 5R6 |
| 5 | 291 | 0.75 | 0.87 | 36 | NI, SIN, 5R6 |
Interfaces
5 interfaces between chains.
- B–C · 699 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 689 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 641 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 112 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5ERL · Crystal structure of the epimerase SnoN in complex with Ni2+, succinate and nogalamycin RO · 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 Q9RN67
- Every structure of UniProt Q9EYI0
- Elsewhere: RCSB PDB 5ERL · PDBe 5ERL · UniProt Q9RN67 · UniProt Q9EYI0
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