MolNFT v1 · #66289 · protein
Crystal structure of the flavodoxin-like domain from synechococcus sp Q5MZP6_SYNP6 protein. northeast structural genomics consortium target SNR135D.
3HLY: “Crystal structure of the flavodoxin-like domain from synechococcus sp Q5MZP6_SYNP6 protein. northeast…”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.58). MolNFT v1 #66289 on GenesisL1: 3D structure, binding…
- PDB
- 3HLY
- Type
- protein
- Length
- 442 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavodoxin-like domain
- UniProt
- Q5MZP6
- Ligands
- CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavodoxin-like domain | protein | 145 | 46% helix, 17% strand | Q5MZP6 |
| B | Flavodoxin-like domain | protein | 144 | 47% helix, 17% strand | Q5MZP6 |
| C | Flavodoxin-like domain | protein | 153 | 46% helix, 16% strand | Q5MZP6 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.58 | 0.75 | 45 | empty |
| 2 | 146 | 0.44 | 0.76 | 20 | empty |
| 3 | 69 | 0.35 | 0.77 | 16 | empty |
| 4 | 78 | 0.32 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 927 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3HLY · Crystal Structure of the Flavodoxin-like domain from Synechococcus sp Q5MZP6_SYNP6… · 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 Q5MZP6
- Elsewhere: RCSB PDB 3HLY · PDBe 3HLY · UniProt Q5MZP6
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