1MBD | pdb_00001mbd

X-ray structure of sperm whale deoxymoglobin refined at 1.4A resolution

• PDB DOI: https://doi.org/10.2210/pdb1MBD/pdb

• Classification: OXYGEN STORAGE
• Organism(s): Physeter macrocephalus
• Mutation(s): No 


• Deposited: 1981-08-27 Released: 1982-02-03 
• Deposition Author(s): Phillips, S.E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å

Literature

X-ray structure of sperm whale deoxymoglobin refined at 1.4A resolution

Phillips, S.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.95 kDa 
• Atom Count: 1,666 
• Modeled Residue Count: 153 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	153	Physeter macrocephalus	Mutation(s): 0  EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.66	α = 90
b = 31.12	β = 105.78
c = 35.06	γ = 90

Software Package:

Software Name	Purpose
CONSTRAINED	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1982-02-03 
Deposition Author(s): Phillips, S.E.V.

Revision History  

• Version 1.0: 1982-02-03
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-08
  Changes: Database references, Other, Structure summary
• Version 2.0: 2023-02-08
  Type: Remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-05-22
  Changes: Data collection