3ZUN | pdb_00003zun

pVHL54-213-EloB-EloC complex_(2S,4R)-4-hydroxy-1-(2-(3-methylisoxazol- 5-yl)acetyl)-N-(4-nitrobenzyl)pyrrolidine-2-carboxamide bound

PDB DOI: https://doi.org/10.2210/pdb3ZUN/pdb

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

Deposited: 2011-07-19 Released: 2012-07-25
Deposition Author(s): Van Molle, I., Buckley, D., Crews, C.M., Ciulli, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.302 (Depositor), 0.292 (DCC)
R-Value Work:
0.229 (Depositor), 0.226 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Elongin-B, Elongin-C, Von Hippel-Lindau Disease Tumor Suppressor Complex

Buckley, D., Van Molle, I., Gareiss, P.C., Tae, H.S., Michel, J., Noblin, D.J., Jorgensen, W.L., Ciulli, A., Crews, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 173.5 kDa
Atom Count: 10,609
Modeled Residue Count: 1,319
Deposited Residue Count: 1,512
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2	A, D, G, J	118	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1	B, E, H, K	97	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR	C, F, I, L	163	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZUN Query on ZUN Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain Q [auth L] SDF format, chain P [auth I] SDF format, chain N [auth C] MOL2 format, chain O [auth F] MOL2 format, chain Q [auth L] MOL2 format, chain P [auth I] MOL2 format, chain N [auth C] mmCIF format, chain O [auth F] mmCIF format, chain Q [auth L] mmCIF format, chain P [auth I] mmCIF format, chain N [auth C]	N [auth C], O [auth F], P [auth I], Q [auth L]	(4R)-4-hydroxy-1-[(3-methyl-1,2-oxazol-5-yl)acetyl]-N-[(4-nitrophenyl)methyl]-L-prolinamide C₁₈ H₂₀ N₄ O₆ CVKGDHXKAUTTSP-ZBFHGGJFSA-N		Interactions Focus chain N [auth C] Focus chain O [auth F] Focus chain P [auth I] Focus chain Q [auth L] Interactions & Density Focus chain N [auth C] Focus chain O [auth F] Focus chain P [auth I] Focus chain Q [auth L]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.302 (Depositor), 0.292 (DCC)
R-Value Work: 0.229 (Depositor), 0.226 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.404	α = 90
b = 93.404	β = 90
c = 362.891	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-25
Type: Initial release
Version 1.1: 2017-12-20
Changes: Database references, Structure summary
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 2.0: 2026-04-15
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary