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The structure of kdgf from halomonas sp.
Analyse The structure of kdgf from halomonas sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FQ0
- Type
- protein
- Length
- 439 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kdgf; Residual cleaved his tag
- Ligands
- NI
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kdgf | protein | 110 | 5% helix, 58% strand | — |
| B | Kdgf | protein | 109 | 6% helix, 59% strand | — |
| C | Kdgf | protein | 109 | 6% helix, 58% strand | — |
| D | Kdgf | protein | 108 | 6% helix, 58% strand | — |
| H | Residual cleaved his tag | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, B, C, D, H
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.65 | 0.85 | 27 | FLC |
| 2 | 171 | 0.64 | 0.85 | 27 | FLC |
| 3 | 155 | 0.64 | 0.85 | 27 | FLC |
| 4 | 252 | 0.64 | 0.82 | 34 | empty |
| 5 | 187 | 0.62 | 0.83 | 26 | FLC |
Interfaces
8 interfaces between chains.
- A–B · 1647 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1552 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 277 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 268 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 230 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FQ0 · The structure of KdgF from Halomonas sp. · 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 5FQ0 · PDBe 5FQ0
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