MolNFT v1 · #15991 · protein
Crystal structure of MURG:GLCNAC complex
1NLM · Udp-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)…: “Crystal structure of MURG:GLCNAC complex”. X-ray diffraction, 1 ligand (UD1), 5 pockets (best druggability 0.80). MolNFT v1 #15991 on GenesisL1: 3D structure, binding sites…
- PDB
- 1NLM
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol…
- EC
- 2.4.1.-
- UniProt
- P17443
- Ligands
- UD1
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (EC 2.4.1.-) | protein | 350 | 48% helix, 17% strand | P17443 |
Ligands and binding sites
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.80 | 0.84 | 51 | GOL |
| 2 | 498 | 0.64 | 0.76 | 63 | UD1, GOL |
| 3 | 424 | 0.60 | 0.75 | 62 | UD1 |
| 4 | 65 | 0.55 | 0.87 | 17 | empty |
| 5 | 58 | 0.53 | 0.87 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 508 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P17443
- Elsewhere: RCSB PDB 1NLM · PDBe 1NLM · UniProt P17443
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