1BP1

CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INCREASING PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1BP1/pdb

• Classification: BACTERICIDAL
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 1997-04-08 Released: 1997-09-04 
• Deposition Author(s): Beamer, L.J., Carroll, S.F., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.295 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

Literature

Crystal structure of human BPI and two bound phospholipids at 2.4 angstrom resolution.

Beamer, L.J., Carroll, S.F., Eisenberg, D.

(1997) Science 276: 1861-1864

• PubMed: 9188532 
• DOI: https://doi.org/10.1126/science.276.5320.1861
• Primary Citation of Related Structures:  
  1BP1


• PubMed Abstract: 
  

  Bactericidal/permeability-increasing protein (BPI), a potent antimicrobial protein of 456 residues, binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria. At a resolution of 2.4 angstroms, the crystal structure of human BPI shows a boomerang-shaped molecule formed by two similar domains. Two apolar pockets on the concave surface of the boomerang each bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. As a model for the related plasma lipid transfer proteins, BPI illuminates a mechanism of lipid transfer for this protein family.

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Organizational Affiliation: 

UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.28 kDa 
• Atom Count: 3,677 
• Modelled Residue Count: 456 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN	A	456	Homo sapiens	Mutation(s): 1  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P17213 (Homo sapiens) Explore P17213  Go to UniProtKB:  P17213
PHAROS:  P17213 GTEx:  ENSG00000101425

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC1	B [auth A], C [auth A]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.295 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 185.6	α = 90
b = 33	β = 101.6
c = 85.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-04 
Deposition Author(s): Beamer, L.J., Carroll, S.F., Eisenberg, D.

Revision History  

• Version 1.0: 1997-09-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary