6F02 | pdb_00006f02

Crystal structure of human glycosylated kallistatin at 3.0 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb6F02/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-11-17 Released: 2018-12-12 
• Deposition Author(s): Zhou, A., Ma, L.
• Funding Organization(s): British Heart Foundation, NSFC

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Kallistatin

Zhou, A., Ma, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.95 kDa 
• Atom Count: 6,212 
• Modeled Residue Count: 745 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallistatin	A, B [auth C]	389	Homo sapiens	Mutation(s): 0  Gene Names: SERPINA4, KST, PI4
UniProt & NIH Common Fund Data Resources
Find proteins for P29622 (Homo sapiens) Explore P29622  Go to UniProtKB:  P29622
PHAROS:  P29622 GTEx:  ENSG00000100665
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P29622-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B], D, E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86566TX GlyCosmos:  G86566TX GlyGen:  G86566TX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61843VN GlyCosmos:  G61843VN GlyGen:  G61843VN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth C], H [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.02	α = 90
b = 138.02	β = 90
c = 157.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Zhou, A., Ma, L.

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Funding Organization	Location	Grant Number
British Heart Foundation	United Kingdom	--
NSFC	China	81572090

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary