MolNFT v1 · #98432 · protein
Crystal structure of the PKD1 domain from vibrio cholerae metalloprotease prtv
4L9D: “Crystal structure of the PKD1 domain from vibrio cholerae metalloprotease prtv”. X-ray diffraction, 3 ligands (NA, CA, CL). MolNFT v1 #98432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4L9D
- Type
- protein
- Length
- 163 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- UniProt
- C3LUP3
- Ligands
- NA, CA, CL
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease | protein | 82 | 0% helix, 57% strand | C3LUP3 |
| B | Protease | protein | 81 | 0% helix, 58% strand | C3LUP3 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 749 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4L9D · Crystal structure of the PKD1 domain from Vibrio cholerae metalloprotease PrtV · the same entry in another collection · chain A against A, TM-score 1.00
- C3LUP3 · AlphaFold monomer V2.0 prediction for pre-pro-metalloprotease prtv (C3LUP3) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 C3LUP3
- Elsewhere: RCSB PDB 4L9D · PDBe 4L9D · UniProt C3LUP3
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