MolNFT v1 · #112510 · protein
X-ray crystallography of recombinant lactococcus lactis prolidase
4ZNG: “X-ray crystallography of recombinant lactococcus lactis prolidase”. X-ray diffraction, 1 ligand (MN), 11 pockets (best druggability 0.77). MolNFT v1 #112510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ZNG
- Type
- protein
- Length
- 1,074 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolidase
- EC
- 3.4.13.9
- UniProt
- A8WBX8
- Ligands
- MN
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Prolidase (EC 3.4.13.9) | protein | 352 | 28% helix, 16% strand | A8WBX8 |
| B | Prolidase (EC 3.4.13.9) | protein | 360 | 39% helix, 22% strand | A8WBX8 |
| A | Prolidase (EC 3.4.13.9) | protein | 362 | 37% helix, 22% strand | A8WBX8 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains C, B, A
- CAC · Cacodylate ion · additive · 2 copies · chains B, A
- GOL · Glycerol · additive · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.77 | 0.79 | 77 | CAC |
| 2 | 428 | 0.62 | 0.76 | 38 | empty |
| 3 | 276 | 0.59 | 0.79 | 36 | GOL |
| 4 | 276 | 0.55 | 0.76 | 33 | MN, CAC |
| 5 | 235 | 0.52 | 0.76 | 26 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1005 Ų buried · 12 hydrogen bonds · protein-protein
- C–A · 493 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4ZNG · X-ray crystallography of recombinant Lactococcus lactis prolidase · the same entry in another collection · chain C against C, 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 A8WBX8
- Elsewhere: RCSB PDB 4ZNG · PDBe 4ZNG · UniProt A8WBX8
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