Research workbench
Glucosamie-6-phosphate deaminase from pasturella multocida
Analyse Glucosamie-6-phosphate deaminase from pasturella multocida in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LQM
- Type
- protein
- Length
- 1,047 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosamine-6-phosphate deaminase
- EC
- 3.5.99.6
- UniProt
- Q9CMF4
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 258 | 45% helix, 17% strand | Q9CMF4 |
| B | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 265 | 44% helix, 16% strand | Q9CMF4 |
| C | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 257 | 44% helix, 17% strand | Q9CMF4 |
| D | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 267 | 44% helix, 16% strand | Q9CMF4 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.79 | 0.81 | 71 | empty |
| 2 | 391 | 0.70 | 0.82 | 40 | empty |
| 3 | 356 | 0.66 | 0.80 | 38 | empty |
| 4 | 258 | 0.61 | 0.80 | 35 | empty |
| 5 | 438 | 0.58 | 0.74 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 523 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 505 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 482 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 128 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7LQM · Glucosamie-6-phosphate Deaminase from Pasturella multocida · the same entry in another collection · chain D against D, TM-score 1.00
- Q9CMF4 · AlphaFold monomer V2.0 prediction for glucosamine-6-phosphate deaminase (Q9CMF4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9CMF4
- Elsewhere: RCSB PDB 7LQM · PDBe 7LQM · UniProt Q9CMF4
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