Research workbench
Murc - crystal structure of the enzyme from haemophilus influenzae complexed with amppcp
Analyse Murc - crystal structure of the enzyme from haemophilus influenzae complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GQY
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramate-L-alanine ligase
- EC
- 6.3.2.8
- UniProt
- P45066
- Ligands
- ACP, MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) | protein | 468 | 40% helix, 25% strand | P45066 |
| B | Udp-N-acetylmuramate-L-alanine ligase (EC 6.3.2.8) | protein | 469 | 36% helix, 25% strand | P45066 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.78 | 0.81 | 95 | ACP, MG |
| 2 | 762 | 0.73 | 0.78 | 96 | ACP, MG |
| 3 | 328 | 0.59 | 0.77 | 39 | empty |
| 4 | 152 | 0.54 | 0.80 | 26 | empty |
| 5 | 220 | 0.53 | 0.77 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1225 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1GQY · Murc - crystal structure of the enzyme from haemophilus influenzae complexed with amppcp · the same entry in another collection · chain A against A, TM-score 1.00
- P45066 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramate--L-alanine ligase (P45066) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P45066
- Elsewhere: RCSB PDB 1GQY · PDBe 1GQY · UniProt P45066
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