8BUT

Structure of DDB1 bound to DS61-engaged CDK12-cyclin K

PDB DOI: https://doi.org/10.2210/pdb8BUT/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2022-11-30 Released: 2023-09-13
Deposition Author(s): Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.
Funding Organization(s): European Research Council (ERC), Swiss National Science Foundation, Swiss Cancer League, Marie Sklodowska-Curie Actions, FragNET ITN, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.217
R-Value Work: 0.197
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of DDB1 bound to DS22-engaged CDK12-cyclin K

Kozicka, Z., Kempf, G., Focht, V., Thoma, N.H.

To be published.

Macromolecule Content

Total Structure Weight: 499.82 kDa
Atom Count: 33,831
Modelled Residue Count: 4,202
Deposited Residue Count: 4,365
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A, D, G	840	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16531
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 12	B, E, H	344	Homo sapiens	Mutation(s): 1 Gene Names: CDK12, CRK7, CRKRS, KIAA0904 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYV4 (Homo sapiens) Explore Q9NYV4 Go to UniProtKB: Q9NYV4
PHAROS: Q9NYV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NYV4
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-K	C, F, I	271	Homo sapiens	Mutation(s): 0 Gene Names: CCNK, CPR4
UniProt & NIH Common Fund Data Resources
Find proteins for O75909 (Homo sapiens) Explore O75909 Go to UniProtKB: O75909
PHAROS: O75909
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75909
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RQ5 (Subject of Investigation/LOI) Query on RQ5 Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain N [auth B] SDF format, chain V [auth E] MOL2 format, chain DA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain V [auth E]	DA [auth H], N [auth B], V [auth E]	2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol C₂₁ H₃₀ N₆ O₃ AFLLXNOWMGJTAA-MRXNPFEDSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain GA [auth I] SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain EA [auth I] SDF format, chain FA [auth I] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain W [auth F] SDF format, chain X [auth F] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth I] MOL2 format, chain FA [auth I] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G]	AA [auth G] BA [auth G] CA [auth G] EA [auth I] FA [auth I] AA [auth G], BA [auth G], CA [auth G], EA [auth I], FA [auth I], GA [auth I], J [auth A], K [auth A], L [auth A], M [auth A], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth D], W [auth F], X [auth F], Y [auth G], Z [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	B, E, H	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.217
R-Value Work: 0.197
R-Value Observed: 0.198
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 249.701	α = 90
b = 249.701	β = 90
c = 218.495	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Coot	model building
STARANISO	data scaling
autoPROC	data processing
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-13

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	666068
Swiss National Science Foundation	Switzerland	31003A_179541
Swiss National Science Foundation	Switzerland	310030_301206
Swiss Cancer League	Switzerland	4980-02-2020
Swiss National Science Foundation	Switzerland	CRSII5_186230
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	765445
Other private	Switzerland	--