MolNFT v1 · #100675 · protein
Crystal structure of N-acetylneuraminate lyase from mycoplasma synoviae, crystal form I
4N4P · Acylneuraminate lyase: “Crystal structure of N-acetylneuraminate lyase from mycoplasma synoviae, crystal form I”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.69). MolNFT v1 #100675 on GenesisL1: 3D structure…
- PDB
- 4N4P
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acylneuraminate lyase
- EC
- 4.1.3.3
- UniProt
- Q4A6K4
- Ligands
- CL
- Pockets
- 12 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acylneuraminate lyase (EC 4.1.3.3) | protein | 290 | 52% helix, 13% strand | Q4A6K4 |
| C | Acylneuraminate lyase (EC 4.1.3.3) | protein | 289 | 52% helix, 13% strand | Q4A6K4 |
| D | Acylneuraminate lyase (EC 4.1.3.3) | protein | 288 | 52% helix, 14% strand | Q4A6K4 |
Ligands and binding sites
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.69 | 0.80 | 52 | empty |
| 2 | 474 | 0.69 | 0.80 | 59 | empty |
| 3 | 496 | 0.62 | 0.75 | 47 | CL |
| 4 | 505 | 0.62 | 0.75 | 44 | CL |
| 5 | 493 | 0.61 | 0.75 | 45 | CL |
Interfaces
4 interfaces between chains.
- A–B · 1247 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1245 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1170 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4N4P · Crystal Structure of N-acetylneuraminate lyase from Mycoplasma synoviae, crystal form I · 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 Q4A6K4
- Elsewhere: RCSB PDB 4N4P · PDBe 4N4P · UniProt Q4A6K4
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