Research workbench
Crystal structure of hygx from streptomyces hygroscopicus with nickel, 2-oxoglutarate, and hygromycin B bound
Analyse Crystal structure of hygx from streptomyces hygroscopicus with nickel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XCB
- Type
- protein
- Length
- 1,024 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- OXIDASE/HYDROXYLASE
- UniProt
- Q2MFS1
- Ligands
- AKG, HY0, NI
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | OXIDASE/HYDROXYLASE | protein | 260 | 24% helix, 27% strand | Q2MFS1 |
| B | OXIDASE/HYDROXYLASE | protein | 259 | 23% helix, 28% strand | Q2MFS1 |
| C | OXIDASE/HYDROXYLASE | protein | 254 | 24% helix, 28% strand | Q2MFS1 |
| D | OXIDASE/HYDROXYLASE | protein | 251 | 21% helix, 29% strand | Q2MFS1 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- HY0 · Hygromycin B variant · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.85 | 0.86 | 75 | empty |
| 2 | 475 | 0.78 | 0.85 | 45 | NI, AKG, HY0 |
| 3 | 443 | 0.78 | 0.86 | 49 | NI, AKG, HY0 |
| 4 | 493 | 0.77 | 0.85 | 54 | NI, AKG, HY0 |
| 5 | 428 | 0.76 | 0.85 | 50 | NI, AKG, HY0 |
Interfaces
6 interfaces between chains.
- C–D · 2104 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2086 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 1350 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1345 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XCB · Crystal Structure of HygX from Streptomyces hygroscopicus with nickel, 2-oxoglutarate… · 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 Q2MFS1
- Elsewhere: RCSB PDB 4XCB · PDBe 4XCB · UniProt Q2MFS1
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