9BKR | pdb_00009bkr

Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb9BKR/pdb
Entry: 9BKR supersedes: 8TRE

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

Deposited: 2024-04-29 Released: 2024-07-31
Deposition Author(s): Kimani, S., Dong, A., Li, Y., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.208 (Depositor), 0.215 (DCC)
R-Value Work:
0.162 (Depositor), 0.172 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of the Human TRIP12 WWE domain (isoform 2) in complex with ATP

Kimani, S., Dong, A., Li, Y., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 9.62 kDa
Atom Count: 765
Modeled Residue Count: 74
Deposited Residue Count: 80
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of E3 ubiquitin-protein ligase TRIP12	A	80	Homo sapiens	Mutation(s): 0 Gene Names: TRIP12, KIAA0045, ULF EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q14669 (Homo sapiens) Explore Q14669 Go to UniProtKB: Q14669
PHAROS: Q14669 GTEx: ENSG00000153827
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.208 (Depositor), 0.215 (DCC)
R-Value Work: 0.162 (Depositor), 0.172 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.351	α = 90
b = 33.492	β = 90
c = 66.081	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

This entry supersedes: 8TRE

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release

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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.