3BX8 | pdb_00003bx8

Engineered Human Lipocalin 2 (LCN2), apo-form

PDB DOI: https://doi.org/10.2210/pdb3BX8/pdb

Classification: DE NOVO PROTEIN, PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-11 Released: 2009-01-20
Deposition Author(s): Schonfeld, D.L., Chatwell, L., Skerra, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.282 (Depositor), 0.290 (DCC)
R-Value Work:
0.251 (Depositor), 0.260 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

High affinity molecular recognition and functional blockade of CTLA-4 by an engineered human lipocalin

Schonfeld, D.L., Matschiner, G., Chatwell, L., Trentmann, S., Schlehuber, S., Hohlbaum, A., Skerra, A.

To be published.

Macromolecule Content

Total Structure Weight: 164.25 kDa
Atom Count: 11,039
Modeled Residue Count: 1,310
Deposited Residue Count: 1,424
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENGINEERED HUMAN LIPOCALIN 2	A, B, C, D, E A, B, C, D, E, F, G, H	178	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE5 Query on PE5 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain P [auth H] SDF format, chain N [auth F] SDF format, chain L [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain P [auth H] MOL2 format, chain N [auth F] MOL2 format, chain L [auth D] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain P [auth H] mmCIF format, chain N [auth F] mmCIF format, chain L [auth D]	J [auth B], K [auth C], L [auth D], N [auth F], P [auth H]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H] Interactions & Density Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth G] SDF format, chain M [auth E] MOL2 format, chain I [auth A] MOL2 format, chain O [auth G] MOL2 format, chain M [auth E] mmCIF format, chain I [auth A] mmCIF format, chain O [auth G] mmCIF format, chain M [auth E]	I [auth A], M [auth E], O [auth G]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain M [auth E] Focus chain O [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.282 (Depositor), 0.290 (DCC)
R-Value Work: 0.251 (Depositor), 0.260 (DCC)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.482	α = 110.77
b = 92.861	β = 90
c = 98.825	γ = 109.36

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-01-20

Deposition Author(s):

Schonfeld, D.L.

Chatwell, L.

Skerra, A.

Revision History (Full details and data files)

Version 1.0: 2009-01-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.3: 2024-11-20
Changes: Structure summary