6F4V | pdb_00006f4v

Crystal structure of cleaved Kallistatin complexed with heparin at 1.8 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb6F4V/pdb

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

Deposited: 2017-11-30 Released: 2018-12-12
Deposition Author(s): Zhou, A., Wei, Z.
Funding Organization(s): British Heart Foundation, NSFC

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.196 (Depositor), 0.207 (DCC)
R-Value Work:
0.172 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of human Kallistatin

Zhou, A., Ma, L.

To be published.

Macromolecule Content

Total Structure Weight: 44.74 kDa
Atom Count: 3,364
Modeled Residue Count: 376
Deposited Residue Count: 381
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallistatin	A	341	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29622
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kallistatin	B [auth G]	40	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29622
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
3-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2,3,6-tri-O-sulfo-alpha-D-glucopyranoside	C [auth B]	2		N/A	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G18182CM GlyCosmos: G18182CM

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth G]	I [auth A], K [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain K [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth G]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.196 (Depositor), 0.207 (DCC)
R-Value Work: 0.172 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.77	α = 90
b = 113.77	β = 90
c = 76.561	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Zhou, A.

Wei, Z.

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

Revision History (Full details and data files)

Version 1.0: 2018-12-12
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-05-08
Changes: Data collection, Database references