2BEL

Structure of human 11-beta-hydroxysteroid dehydrogenase in complex with NADP and carbenoxolone

PDB DOI: https://doi.org/10.2210/pdb2BEL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-11-25 Released: 2004-12-06
Deposition Author(s): Kavanagh, K., Wu, X., Svensson, S., Elleby, B., von Delft, F., Debreczeni, J.E., Sharma, S., Bray, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Abrahmsen, L., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.246
R-Value Work: 0.188
R-Value Observed: 0.190

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The High Resolution Structures of Human, Murine and Guinea Pig 11-Beta-Hydroxysteroid Dehydrogenase Type 1 Reveal Critical Differences in Active Site Architecture

Wu, X., Kavanagh, K., Svensson, S., Elleby, B., Hult, M., von Delft, F., Marsden, B., Jornvall, H., Abrahmsen, L., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 129.82 kDa
Atom Count: 8,071
Modelled Residue Count: 1,001
Deposited Residue Count: 1,132
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1	A, B, C, D	283	Homo sapiens	Mutation(s): 0 EC: 1.1.1.146 (PDB Primary Data), 1.1.1.201 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28845 (Homo sapiens) Explore P28845 Go to UniProtKB: P28845
PHAROS: P28845 GTEx: ENSG00000117594
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28845
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
CBO Query on CBO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D]	F [auth A], I [auth B], L [auth C], O [auth D]	CARBENOXOLONE C₃₄ H₅₀ O₇ OBZHEBDUNPOCJG-WBXJDKIVSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	G [auth A], J [auth B], M [auth C], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
CBO	BindingDB: 2BEL	Ki: 62 (nM) from 1 assay(s)
CBO	BindingDB: 2BEL	IC50: min: 40, max: 1630 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.246
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.162	α = 90
b = 112.984	β = 90
c = 66.326	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-12-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-12-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-05-01
Changes: Data collection, Database references, Other, Refinement description

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Help and Resources

2BEL

Structure of human 11-beta-hydroxysteroid dehydrogenase in complex with NADP and carbenoxolone

The High Resolution Structures of Human, Murine and Guinea Pig 11-Beta-Hydroxysteroid Dehydrogenase Type 1 Reveal Critical Differences in Active Site Architecture

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)