MolNFT v1 · #99332 · protein
Crystal structure of murq from H.INFLUENZAE in apo form
4M0D · N-acetylmuramic acid 6-phosphate etherase: “Crystal structure of murq from H.INFLUENZAE in apo form”. X-ray diffraction, 10 pockets (best druggability 0.85). MolNFT v1 #99332 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4M0D
- Type
- protein
- Length
- 1,186 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
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 299 | 52% helix, 9% strand | P44862 |
| B | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 291 | 54% helix, 9% strand | P44862 |
| C | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 297 | 50% helix, 9% strand | P44862 |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.85 | 0.86 | 89 | empty |
| 2 | 250 | 0.83 | 0.96 | 42 | empty |
| 3 | 253 | 0.83 | 0.95 | 41 | empty |
| 4 | 239 | 0.83 | 0.96 | 40 | empty |
| 5 | 245 | 0.82 | 0.95 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–D · 4480 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 4374 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 278 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 262 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 93 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4M0D · Crystal structure of MurQ from H.influenzae in apo form · the same entry in another collection · chain A against A, 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 4M0D · PDBe 4M0D · UniProt P44862
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