Research workbench
Crystal structure of murd ligase in complex with D-glu containing sulfonamide inhibitor
Analyse Crystal structure of murd ligase in complex with D-glu containing sulfonamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VTE
- Type
- protein
- Length
- 433 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
- IK4, SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% 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 | 35% helix, 22% strand | P14900 |
Ligands and binding sites
- IK4 · N-({7-[(4-cyanobenzyl)oxy]naphthalen-2-yl}sulfonyl)-D-glutamic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.75 | 0.79 | 73 | IK4, SO4 |
| 2 | 232 | 0.53 | 0.77 | 25 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, carboxylation).
Compared structures
- 2VTE · 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 2VTE · PDBe 2VTE · UniProt P14900
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