3WCP | pdb_00003wcp

Deoxyhemoglobin SH-drug complex

• PDB DOI: https://doi.org/10.2210/pdb3WCP/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-05-30 Released: 2013-06-26 
• Deposition Author(s): Safo, M.K., Ko, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.263 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Deoxyhemoglobin SH-drug complex

Safo, M.K., Ko, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 65.14 kDa 
• Atom Count: 5,262 
• Modeled Residue Count: 572 
• Deposited Residue Count: 574 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905  Go to UniProtKB:  P69905
PHAROS:  P69905 GTEx:  ENSG00000188536 ENSG00000206172

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	146	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871  Go to UniProtKB:  P68871
PHAROS:  P68871 GTEx:  ENSG00000244734

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], F [auth B], I [auth C], J [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DG2	G [auth B], H [auth B]	(2R)-2,3-diphosphoglyceric acid C3 H8 O10 P2 XOHUEYCVLUUEJJ-UWTATZPHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	B, D	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.263 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.719	α = 90
b = 96.924	β = 90
c = 65.087	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Safo, M.K., Ko, T.P.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Non-polymer description
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary