MolNFT v1 · #170587 · protein
Structure of adenylylated C. glutamicum glnk
6YC7 · Pii protein: “Structure of adenylylated C. glutamicum glnk”. X-ray diffraction, 3 ligands (A5O, AMP, ADP), 9 pockets (best druggability 0.88). MolNFT v1 #170587 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YC7
- Type
- protein
- Length
- 605 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pii protein
- UniProt
- H7C694
- Ligands
- A5O, AMP, ADP
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Pii protein | protein | 105 | 30% helix, 37% strand | H7C694 |
| B | Pii protein | protein | 105 | 30% helix, 38% strand | H7C694 |
| C | Pii protein | protein | 96 | 33% helix, 38% strand | H7C694 |
| D | Pii protein | protein | 100 | 32% helix, 36% strand | H7C694 |
| F | Pii protein | protein | 94 | 31% helix, 37% strand | H7C694 |
Ligands and binding sites
- A5O · Adenine arabinose-5'-phosphate · ligand · 3 copies · chains A, C, D, F, B, E
- AMP · Adenosine monophosphate · ligand · chains B, C
- ADP · Adenosine-5'-diphosphate · ligand · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.88 | 0.89 | 104 | A5O |
| 2 | 78 | 0.75 | 0.98 | 18 | empty |
| 3 | 80 | 0.73 | 0.96 | 18 | empty |
| 4 | 256 | 0.63 | 0.81 | 35 | empty |
| 5 | 240 | 0.62 | 0.81 | 35 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1227 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1216 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1197 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1121 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1084 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6YC7 · Structure of adenylylated C. glutamicum GlnK · 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 H7C694
- Elsewhere: RCSB PDB 6YC7 · PDBe 6YC7 · UniProt H7C694
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