1SQY | pdb_00001sqy

Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5

• PDB DOI: https://doi.org/10.2210/pdb1SQY/pdb

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


• Deposited: 2004-03-22 Released: 2004-04-13 
• Deposition Author(s): Vikram, P., Prem Kumar, R., Singh, N., Kumar, J., Ethayathulla, A.S., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.215 (Depositor) 
• R-Value Work: 
  0.204 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5.

Vikram, P., Prem Kumar, R., Singh, N., Kumar, J., Ethayathulla, A.S., Sharma, S., Kaur, P., Singh, T.P.

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: 77.37 kDa 
• Atom Count: 5,719 
• Modeled Residue Count: 691 
• Deposited Residue Count: 691 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lactoferrin	A	691	Homo sapiens	Mutation(s): 0  EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for P02788 (Homo sapiens) Explore P02788  Go to UniProtKB:  P02788
PHAROS:  P02788 GTEx:  ENSG00000012223
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P02788-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO3	F [auth A], G [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	D [auth A], E [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.215 (Depositor) 
• R-Value Work:  0.204 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.156	α = 90
b = 98.09	β = 90
c = 157.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-13 
Deposition Author(s): Vikram, P., Prem Kumar, R., Singh, N., Kumar, J., Ethayathulla, A.S., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2004-04-13
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary