MolNFT v1 · #183948 · protein
Dife-sulerythrin reduced with na-dithionite
7O8A: “Dife-sulerythrin reduced with na-dithionite”. X-ray diffraction, 2 ligands (FE, CL), 6 pockets (best druggability 0.49). MolNFT v1 #183948 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7O8A
- Type
- protein
- Length
- 426 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulerythrin
- UniProt
- F9VPE5
- Ligands
- FE, CL
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 81% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulerythrin | protein | 143 | 80% helix, 0% strand | F9VPE5 |
| B | Sulerythrin | protein | 143 | 82% helix, 0% strand | F9VPE5 |
| C | Sulerythrin | protein | 140 | 81% helix, 0% strand | F9VPE5 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, C, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.49 | 0.74 | 34 | BTB |
| 2 | 88 | 0.40 | 0.77 | 19 | empty |
| 3 | 69 | 0.39 | 0.79 | 17 | empty |
| 4 | 53 | 0.32 | 0.77 | 13 | empty |
| 5 | 72 | 0.31 | 0.74 | 13 | CL |
Interfaces
3 interfaces between chains.
- B–C · 3568 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 530 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 257 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7O8A · diFe-sulerythrin reduced with Na-dithionite · 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 F9VPE5
- Elsewhere: RCSB PDB 7O8A · PDBe 7O8A · UniProt F9VPE5
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