6Z2C | pdb_00006z2c

Engineered lipocalin C3A5 in complex with a transition state analog

PDB DOI: https://doi.org/10.2210/pdb6Z2C/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-05-15 Released: 2021-05-26
Deposition Author(s): Skerra, A., Eichinger, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.194 (DCC)
R-Value Work:
0.161 (Depositor), 0.166 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6Z2C

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of an engineered lipocalin that catalyzes a Diels-Alder reaction

Eichinger, A., Skerra, A.

To be published.

Macromolecule Content

Total Structure Weight: 66.91 kDa
Atom Count: 4,718
Modeled Residue Count: 531
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil gelatinase-associated lipocalin	A, B, C	188	Homo sapiens	Mutation(s): 21 Gene Names: LCN2, HNL, NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188 Go to UniProtKB: P80188
PHAROS: P80188 GTEx: ENSG00000148346
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80188
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q5E (Subject of Investigation/LOI) Query on Q5E Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	1,7,8,9,10,10-hexachloro-4-carboxypentyl-4-aza-tricyclo[5.2.1.0(2,6)]dec-8-ene-3,5-dione C₁₅ H₁₃ Cl₆ N O₄ JIUILXIUOXTHCP-ZPAAZFHLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190 (Depositor), 0.194 (DCC)
R-Value Work: 0.161 (Depositor), 0.166 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.385	α = 90
b = 39.034	β = 120
c = 96.385	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-05-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-05-26
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.