MolNFT v1 · #126245 · protein
Cys-gly dipeptidase glij (space group C2)
5LWZ: “Cys-gly dipeptidase glij (space group C2)”. X-ray diffraction, 1 ligand (FE), 14 pockets (best druggability 0.67). MolNFT v1 #126245 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5LWZ
- Type
- protein
- Length
- 1,145 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- EC
- 3.4.13.19
- UniProt
- Q4WMJ8
- Ligands
- FE
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dipeptidase (EC 3.4.13.19) | protein | 382 | 51% helix, 12% strand | Q4WMJ8 |
| B | Dipeptidase (EC 3.4.13.19) | protein | 381 | 51% helix, 12% strand | Q4WMJ8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.67 | 0.75 | 64 | GOL |
| 2 | 188 | 0.55 | 0.80 | 32 | empty |
| 3 | 201 | 0.49 | 0.75 | 27 | FE |
| 4 | 230 | 0.48 | 0.74 | 28 | FE |
| 5 | 93 | 0.46 | 0.81 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3249 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 676 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
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 Q4WMJ8
- Elsewhere: RCSB PDB 5LWZ · PDBe 5LWZ · UniProt Q4WMJ8
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