MolNFT v1 · #123944 · protein
Structure of an oxidoreductase from synechocystis sp. PCC6803
5K0A · SLR0600 protein: “Structure of an oxidoreductase from synechocystis sp. PCC6803”. X-ray diffraction, 3 ligands (FAD, NO3, PO4), 10 pockets (best druggability 0.88). MolNFT v1 #123944 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K0A
- Type
- protein
- Length
- 1,276 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SLR0600 protein
- UniProt
- P74746
- Ligands
- FAD, NO3, PO4
- Pockets
- 10 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SLR0600 protein | protein | 320 | 30% helix, 29% strand | P74746 |
| B | SLR0600 protein | protein | 321 | 28% helix, 29% strand | P74746 |
| C | SLR0600 protein | protein | 313 | 28% helix, 30% strand | P74746 |
| D | SLR0600 protein | protein | 322 | 30% helix, 29% strand | P74746 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
- PG4 · Tetraethylene glycol · additive · 6 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 5 copies · chains B, C, D
- PGE · Triethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.88 | 0.89 | 139 | FAD, NO3 |
| 2 | 418 | 0.81 | 0.89 | 67 | FAD |
| 3 | 469 | 0.80 | 0.87 | 66 | FAD |
| 4 | 233 | 0.64 | 0.83 | 29 | empty |
| 5 | 232 | 0.64 | 0.82 | 27 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2949 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2944 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 150 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5K0A · Structure of an oxidoreductase from Synechocystis sp. PCC6803 · 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 P74746
- Elsewhere: RCSB PDB 5K0A · PDBe 5K0A · UniProt P74746
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