5HGC | pdb_00005hgc

A Serpin structure

• PDB DOI: https://doi.org/10.2210/pdb5HGC/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Taeniopygia guttata
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-08 Released: 2016-04-06 
• Deposition Author(s): Das, S., Vashchenko, G.V., Van Petegem, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

A Serpin structure

Vashchenko, G.V., Das, S., Moon, K.-M., Rogalski, J.C., Taves, M.D., Soma, K.K., Van Petegem, F., Foster, L.J., Hammond, G.L.

(2016) J Biological Chem 

• DOI: https://doi.org/10.1074/jbc.M116.714378

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.86 kDa 
• Atom Count: 3,240 
• Modeled Residue Count: 373 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serpin	A	380	Taeniopygia guttata	Mutation(s): 0  Gene Names: SERPINA12-1
UniProt
Find proteins for H0ZQY2 (Taeniopygia guttata) Explore H0ZQY2  Go to UniProtKB:  H0ZQY2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCY	B [auth A]	(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione C21 H30 O5 JYGXADMDTFJGBT-VWUMJDOOSA-N
BDG	F [auth A]	2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose C6 H14 N2 O4 SQTHUUHOUPJYLK-UKFBFLRUSA-N
SO4	C [auth A], D [auth A], E [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.15	α = 90
b = 116.15	β = 90
c = 72.73	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Das, S., Vashchenko, G.V., Van Petegem, F.

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary