MolNFT v1 · #157816 · protein
2.05 ångström resolution crystal structure of hypothetical protein KP1_5497 from klebsiella pneumoniae.
6NBG · Glucosamine-6-phosphate deaminase: “2.05 ångström resolution crystal structure of hypothetical protein KP1_5497 from klebsiella pneumoniae.”. X-ray diffraction, 2 ligands (PO4, CL), 20 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 6NBG
- Type
- protein
- Length
- 1,442 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
- A0A332QZQ2
- Ligands
- PO4, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 242 | 38% helix, 21% strand | A0A332QZQ2 |
| B | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 241 | 38% helix, 20% strand | A0A332QZQ2 |
| C, E | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 240 | 37% helix, 20% strand | A0A332QZQ2 |
| D | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 239 | 38% helix, 20% strand | A0A332QZQ2 |
| F | Glucosamine-6-phosphate deaminase (EC 3.5.99.6) | protein | 240 | 37% helix, 20% strand | A0A332QZQ2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.77 | 0.81 | 102 | empty |
| 2 | 62 | 0.69 | 0.96 | 19 | empty |
| 3 | 271 | 0.66 | 0.82 | 36 | PO4 |
| 4 | 824 | 0.64 | 0.73 | 79 | empty |
| 5 | 298 | 0.64 | 0.80 | 32 | PO4 |
Interfaces
13 interfaces between chains.
- C–E · 957 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 926 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 867 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 286 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 6NBG · 2.05 Angstrom Resolution Crystal Structure of Hypothetical Protein KP1_5497 from… · 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 A0A332QZQ2
- Elsewhere: RCSB PDB 6NBG · PDBe 6NBG · UniProt A0A332QZQ2
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