Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 

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This is version 1.5 of the entry. See complete history


The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold.

Kleiger, G.Beamer, L.J.Grothe, R.Mallick, P.Eisenberg, D.

(2000) J Mol Biol 299: 1019-1034

  • DOI: https://doi.org/10.1006/jmbi.2000.3805
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have extended the resolution of the crystal structure of human bactericidal/permeability-increasing protein (BPI) to 1.7 A. BPI has two domains with the same fold, but with little sequence similarity. To understand the similarity in structure of the two domains, we compare the corresponding residue positions in the two domains by the method of 3D-1D profiles. A 3D-1D profile is a string formed by assigning each position in the 3D structure to one of 18 environment classes. The environment classes are defined by the local secondary structure, the area of the residue which is buried from solvent, and the fraction of the area buried by polar atoms. A structural alignment between the two BPI domains was used to compare the 3D-1D environments of structurally equivalent positions. Greater than 31% of the aligned positions have conserved 3D-1D environments, but only 13% have conserved residue identities. Analysis of the 3D-1D environmentally conserved positions helps to identify pairs of residues likely to be important in conserving the fold, regardless of the residue similarity. We find examples of 3D-1D environmentally conserved positions with dissimilar residues which nevertheless play similar structural roles. To generalize our findings, we analyzed four other proteins with similar structures yet dissimilar sequences. Together, these examples show that aligned pairs of dissimilar residues often share similar structural roles, stabilizing dissimilar sequences in the same fold.

  • Organizational Affiliation

    UCLA-DOE Laboratory of Structural Biology and Molecular Medicine, Molecular Biology Institute, Los Angeles, CA, 90095-1570, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P17213 (Homo sapiens)
Explore P17213 
Go to UniProtKB:  P17213
PHAROS:  P17213
GTEx:  ENSG00000101425 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17213
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PC1

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C44 H88 N O8 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.32α = 90
b = 31.23β = 103.2
c = 80.66γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Database references
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2021-11-03
    Changes: Database references, Derived calculations