8BB3 | pdb_00008bb3

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1)

PDB DOI: https://doi.org/10.2210/pdb8BB3/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-12 Released: 2022-11-09
Deposition Author(s): Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)
Funding Organization(s): The Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.193 (Depositor), 0.196 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1)

Kraemer, A., Doelle, A., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 79.91 kDa
Atom Count: 5,513
Modeled Residue Count: 642
Deposited Residue Count: 685
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A [auth J]	104	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
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
Elongin-C	B [auth K]	98	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
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 [auth L]	162	Homo sapiens	Mutation(s): 0 Gene Names: VHL
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

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	D [auth B]	321	Homo sapiens	Mutation(s): 0 Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964 Go to UniProtKB: P61964
PHAROS: P61964 GTEx: ENSG00000196363
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q3X (Subject of Investigation/LOI) Query on Q3X Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide C₅₈ H₇₂ F₃ N₉ O₁₁ S MZOFELXFRDGDBN-GYPJNVOQSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain J [auth K] MOL2 format, chain J [auth K] mmCIF format, chain J [auth K]	J [auth K]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain J [auth K] Interactions & Density Focus chain J [auth K]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain GA [auth B] SDF format, chain I [auth J] SDF format, chain T [auth L] SDF format, chain U [auth B] SDF format, chain S [auth L] SDF format, chain L [auth K] SDF format, chain HA [auth B] SDF format, chain H [auth J] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth J] MOL2 format, chain T [auth L] MOL2 format, chain U [auth B] MOL2 format, chain S [auth L] MOL2 format, chain L [auth K] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth J] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth J] mmCIF format, chain T [auth L] mmCIF format, chain U [auth B] mmCIF format, chain S [auth L] mmCIF format, chain L [auth K] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth J] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], H [auth J], HA [auth B], I [auth J], L [auth K], S [auth L], T [auth L], U [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth J] Focus chain HA [auth B] Focus chain I [auth J] Focus chain L [auth K] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain H [auth J] Focus chain HA [auth B] Focus chain I [auth J] Focus chain L [auth K] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth B]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain R [auth L] SDF format, chain Q [auth L] SDF format, chain P [auth L] SDF format, chain O [auth L] SDF format, chain N [auth L] SDF format, chain M [auth L] SDF format, chain K SDF format, chain G [auth J] SDF format, chain F [auth J] SDF format, chain E [auth J] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain R [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain P [auth L] MOL2 format, chain O [auth L] MOL2 format, chain N [auth L] MOL2 format, chain M [auth L] MOL2 format, chain K MOL2 format, chain G [auth J] MOL2 format, chain F [auth J] MOL2 format, chain E [auth J] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain R [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain P [auth L] mmCIF format, chain O [auth L] mmCIF format, chain N [auth L] mmCIF format, chain M [auth L] mmCIF format, chain K mmCIF format, chain G [auth J] mmCIF format, chain F [auth J] mmCIF format, chain E [auth J]	E [auth J] F [auth J] G [auth J] K M [auth L] E [auth J], F [auth J], G [auth J], K, M [auth L], N [auth L], O [auth L], P [auth L], Q [auth L], R [auth L], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain E [auth J] Focus chain F [auth J] Focus chain G [auth J] Focus chain K Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain E [auth J] Focus chain F [auth J] Focus chain G [auth J] Focus chain K Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]