6KZF | pdb_00006kzf

Racemic X-ray Structure of Calcicludine

• PDB DOI: https://doi.org/10.2210/pdb6KZF/pdb

• Classification: TOXIN
• Organism(s): Dendroaspis angusticeps
• Mutation(s): No 


• Deposited: 2019-09-24 Released: 2019-11-06 
• Deposition Author(s): Qu, Q., Gao, S., Liu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 
  0.282 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.245 (DCC) 

Starting Model: experimental

Literature

Synthesis of Disulfide Surrogate Peptides Incorporating Large-Span Surrogate Bridges Through a Native-Chemical-Ligation-Assisted Diaminodiacid Strategy

Qu, Q., Gao, S., Wu, F., Zhang, M.G., Li, Y., Zhang, L.H., Bierer, D., Tian, C.L., Zheng, J.S., Liu, L.

(2020) Angew Chem Int Ed Engl 59: 6037-6045

• DOI: https://doi.org/10.1002/anie.201915358

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.97 kDa 
• Atom Count: 1,043 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kunitz-type serine protease inhibitor homolog calcicludine	A	60	Dendroaspis angusticeps	Mutation(s): 0
UniProt
Find proteins for P81658 (Dendroaspis angusticeps) Explore P81658  Go to UniProtKB:  P81658

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-calcicludine	B	60	Dendroaspis angusticeps	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DCY	B	D-PEPTIDE LINKING	C3 H7 N O2 S		--
DGL	B	D-PEPTIDE LINKING	C5 H9 N O4		--
DGN	B	D-PEPTIDE LINKING	C5 H10 N2 O3		--
DIL	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DLE	B	D-PEPTIDE LINKING	C6 H13 N O2		--
DLY	B	D-PEPTIDE LINKING	C6 H14 N2 O2		--
DPN	B	D-PEPTIDE LINKING	C9 H11 N O2		--
DPR	B	D-PEPTIDE LINKING	C5 H9 N O2		--
DSG	B	D-PEPTIDE LINKING	C4 H8 N2 O3		--
DSN	B	D-PEPTIDE LINKING	C3 H7 N O3		--
DTH	B	D-PEPTIDE LINKING	C4 H9 N O3		--
DTR	B	D-PEPTIDE LINKING	C11 H12 N2 O2		--
DTY	B	D-PEPTIDE LINKING	C9 H11 N O3		--
DVA	B	D-PEPTIDE LINKING	C5 H11 N O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free:  0.282 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.245 (DCC) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.6	α = 90
b = 94.6	β = 90
c = 38.562	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Qu, Q., Gao, S., Liu, L.

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description