MolNFT v1 · #188662 · protein
Crystal structure of udp-N-acetylmuramoylalanine--D-glutamate ligase (murd) from pseudomonas aeruginosa PAO1 in complex with ADP
7U35: “Crystal structure of udp-N-acetylmuramoylalanine--D-glutamate ligase (murd) from pseudomonas aeruginosa PAO1…”. X-ray diffraction, 1 ligand (ADP), 14 pockets (best druggability 0.76). MolNFT v1 #188662 on GenesisL1: 3D structure…
- PDB
- 7U35
- Type
- protein
- Length
- 1,293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoylalanine--D-glutamate ligase
- EC
- 6.3.2.9
- UniProt
- Q9HVZ9
- Ligands
- ADP
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 429 | 37% helix, 22% strand | Q9HVZ9 |
| B | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 437 | 37% helix, 22% strand | Q9HVZ9 |
| C | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 427 | 37% helix, 23% strand | Q9HVZ9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.76 | 0.90 | 31 | empty |
| 2 | 512 | 0.75 | 0.83 | 56 | empty |
| 3 | 685 | 0.74 | 0.80 | 74 | ADP |
| 4 | 284 | 0.74 | 0.87 | 50 | empty |
| 5 | 839 | 0.71 | 0.77 | 80 | ADP |
Interfaces
3 interfaces between chains.
- A–C · 906 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 745 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 303 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7U35 · 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 0.90
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 7U35 · PDBe 7U35 · UniProt Q9HVZ9
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