MolNFT v1 · #51006 · protein
Crystal structure of murd ligase in complex with D-glu containing sulfonamide inhibitor
2UUP · Udp-N-acetylmuramoylalanine--D-glutamate ligase: “Crystal structure of murd ligase in complex with D-glu containing sulfonamide inhibitor”. X-ray diffraction, 2 ligands (LK4, SO4), 3 pockets (best druggability 0.70). MolNFT v1…
- PDB
- 2UUP
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- 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
- P14900
- Ligands
- LK4, SO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 439 | 35% helix, 21% strand | P14900 |
Ligands and binding sites
- LK4 · N-({6-[(4-cyanobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.70 | 0.78 | 56 | LK4 |
| 2 | 356 | 0.61 | 0.77 | 44 | SO4 |
| 3 | 55 | 0.29 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, carboxylation).
Compared structures
- 2UUP · Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P14900 · 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 0.96
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 P14900
- Elsewhere: RCSB PDB 2UUP · PDBe 2UUP · UniProt P14900
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.