Research workbench
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
Analyse Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SY9
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847…
- Molecule
- UDP-N-acetylmuramoylalanine--D-glutamate ligase
- EC
- 6.3.2.9
- UniProt
- Q9HVZ9
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · resolution 2.75 · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 433 | 39% helix, 22% strand | Q9HVZ9 |
| B | UDP-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 425 | 39% helix, 22% strand | Q9HVZ9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.62 | 0.79 | 39 | empty |
| 2 | 188 | 0.58 | 0.81 | 45 | empty |
| 3 | 292 | 0.54 | 0.75 | 34 | empty |
| 4 | 191 | 0.52 | 0.78 | 27 | empty |
| 5 | 190 | 0.50 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 444 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7SY9 · Crystal structure of udp-N-acetylmuramoylalanine--D-glutamate ligase (murd) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HVZ9 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoylalanine-- D-glutamate ligase… · a predicted model of the same protein · chain A against A, TM-score 0.77
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 Q9HVZ9
- Elsewhere: RCSB PDB 7SY9 · PDBe 7SY9 · UniProt Q9HVZ9
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