7OBF | pdb_00007obf

Crystal structure of the human VH antibody domain HEL4

• PDB DOI: https://doi.org/10.2210/pdb7OBF/pdb

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


• Deposited: 2021-04-22 Released: 2021-05-05 
• Deposition Author(s): Belviso, B.D., Caliandro, R., Carrozzini, B.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human VH antibody domain HEL4

Belviso, B.D., Caliandro, R., Carrozzini, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.55 kDa 
• Atom Count: 1,984 
• Modeled Residue Count: 245 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEL4	A, B	125	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
SO4	G [auth A], H [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.08	α = 90
b = 76.08	β = 90
c = 187.216	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
Sir2014	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Belviso, B.D., Caliandro, R., Carrozzini, B.

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Funding Organization	Location	Grant Number
European Commission	European Union	712965

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary