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Crystal structure of the PKD1 domain from vibrio cholerae metalloprotease prtv

Analyse Crystal structure of the PKD1 domain from vibrio cholerae metalloprotease prtv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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 Å² 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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