Research workbench
Crystal structure of glucosamine-6-phosphate deaminase from borrelia burgdorferi
Analyse Crystal structure of glucosamine-6-phosphate deaminase from borrelia burgdorferi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HN6
- Type
- protein
- Length
- 1,610 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine-6-phosphate deaminase
- EC
- 3.5.99.6
- UniProt
- O30564
- Ligands
- POP
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 271 | 41% helix, 18% strand | O30564 |
| B, D | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 270 | 43% helix, 17% strand | O30564 |
| E | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 266 | 40% helix, 18% strand | O30564 |
| F | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 262 | 40% helix, 18% strand | O30564 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains A, B, C, E, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.69 | 0.86 | 31 | empty |
| 2 | 260 | 0.66 | 0.83 | 34 | empty |
| 3 | 204 | 0.66 | 0.85 | 30 | empty |
| 4 | 234 | 0.66 | 0.83 | 30 | empty |
| 5 | 241 | 0.66 | 0.83 | 35 | empty |
Interfaces
12 interfaces between chains.
- D–F · 998 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 953 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 951 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 948 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 942 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3HN6 · Crystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi · the same entry in another collection · chain F against F, TM-score 1.00
- O30564 · AlphaFold monomer V2.0 prediction for glucosamine-6-phosphate deaminase (O30564) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O30564
- Elsewhere: RCSB PDB 3HN6 · PDBe 3HN6 · UniProt O30564
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