7EIY

Human histidine decarboxylase mutant Y334F soaking with histidine

• PDB DOI: https://doi.org/10.2210/pdb7EIY/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-04-01 Released: 2022-04-06 
• Deposition Author(s): Komori, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.167 

Literature

Structural analysis of the HDC Y334F mutant

Komori, H., Nitta, Y.

(2021) J Biol Macromol 21: 69-74

• DOI: https://doi.org/10.14533/jbm.21.69

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 109.53 kDa 
• Atom Count: 7,731 
• Modelled Residue Count: 933 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine decarboxylase	A, B	481	Homo sapiens	Mutation(s): 2  Gene Names: HDC EC: 4.1.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for P19113 (Homo sapiens) Explore P19113  Go to UniProtKB:  P19113
PHAROS:  P19113 GTEx:  ENSG00000140287

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
HIS	D [auth A], G [auth B]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.93	α = 90
b = 84.998	β = 90
c = 187.417	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Komori, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16K07272

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Database references, Derived calculations