Research workbench
The crystal structure of udp-N-ACETYLMURAMATE:L-alanyl-gamma-D- glutamyl-meso-diaminopimelate ligase (mpl) from neisseria meningitides
Analyse The crystal structure of udp-N-ACETYLMURAMATE:L-alanyl-gamma-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EAG
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-ACETYLMURAMATE:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase
- EC
- 6.3.2.-
- UniProt
- Q9JRY9
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-N-ACETYLMURAMATE:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase (EC 6.3.2.-) | protein | 324 | 33% helix, 24% strand | Q9JRY9 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.66 | 0.83 | 39 | GOL |
| 2 | 275 | 0.64 | 0.81 | 37 | GOL |
| 3 | 225 | 0.57 | 0.79 | 28 | empty |
| 4 | 76 | 0.41 | 0.80 | 17 | empty |
| 5 | 96 | 0.41 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3EAG · The crystal structure of UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimela… · 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 Q9JRY9
- Elsewhere: RCSB PDB 3EAG · PDBe 3EAG · UniProt Q9JRY9
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