MolNFT v1 · #66423 · protein

Ccdb dimer in complex with one C-terminal ccda domain

3HPW · Cytotoxic protein ccdb: “Ccdb dimer in complex with one C-terminal ccda domain”. X-ray diffraction, 1 ligand (SO4). MolNFT v1 #66423 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3HPW
Type: protein
Length: 235 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytotoxic protein ccdb; Protein ccda
UniProt: P62554, P62552
Ligands: SO4

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytotoxic protein ccdb	protein	101	25% helix, 38% strand	P62554
C	Protein ccda	protein	33	82% helix, 0% strand	P62552

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B
PEG · Di(hydroxyethyl)ether · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

3 interfaces between chains.

A–B · 964 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 934 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 625 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3HPW · CcdB dimer in complex with one C-terminal CcdA domain · the same entry in another collection · chain A against A, TM-score 1.00
P62554 · AlphaFold monomer V2.0 prediction for toxin ccdb (P62554) · a predicted model of the same protein · chain B against A, TM-score 0.98
P62552 · AlphaFold monomer V2.0 prediction for antitoxin ccda (P62552) · a predicted model of the same protein · chain C against A, TM-score 0.68

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 P62554
Every structure of UniProt P62552
Elsewhere: RCSB PDB 3HPW · PDBe 3HPW · UniProt P62554 · UniProt P62552

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