MolNFT v1 · #99305 · protein
Crystal structure of murq from H.INFLUENZAE with bound inhibitor
4LZJ · N-acetylmuramic acid 6-phosphate etherase: “Crystal structure of murq from H.INFLUENZAE with bound inhibitor”. X-ray diffraction, 2 ligands (22H, PO4), 13 pockets (best druggability 0.81). MolNFT v1 #99305 on GenesisL1: 3D…
- PDB
- 4LZJ
- Type
- protein
- Length
- 1,174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmuramic acid 6-phosphate etherase
- EC
- 4.2.1.126
- UniProt
- P44862
- Ligands
- 22H, PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 293 | 56% helix, 9% strand | P44862 |
| B | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 299 | 54% helix, 9% strand | P44862 |
| C | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 285 | 51% helix, 9% strand | P44862 |
| D | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 297 | 55% helix, 10% strand | P44862 |
Ligands and binding sites
- 22H · 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-6-O-phosphono-D-glucitol · ligand · 2 copies · chains B, C, A, D
- PO4 · Phosphate ion · ion · 2 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.96 | 38 | 22H |
| 2 | 176 | 0.81 | 0.96 | 40 | 22H |
| 3 | 167 | 0.80 | 0.96 | 33 | PO4 |
| 4 | 849 | 0.75 | 0.79 | 65 | empty |
| 5 | 389 | 0.73 | 0.84 | 59 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4494 Ų buried · 78 hydrogen bonds · protein-protein
- A–D · 3956 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 272 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4LZJ · Crystal Structure of MurQ from H.influenzae with bound inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P44862 · AlphaFold monomer V2.0 prediction for N-acetylmuramic acid 6-phosphate etherase (P44862) · a predicted model of the same protein · chain B 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 P44862
- Elsewhere: RCSB PDB 4LZJ · PDBe 4LZJ · UniProt P44862
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