6GR8 | pdb_00006gr8

Human AURKC INCENP complex bound to BRD-7880

PDB DOI: https://doi.org/10.2210/pdb6GR8/pdb

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

Deposited: 2018-06-10 Released: 2019-05-15
Deposition Author(s): Abdul Azeez, K.R., Sorrell, F.J., von Delft, F., Bountra, C., Knapp, S., Edwards, A.M., Arrowsmith, C., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.216 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

AURKC INCENP complex bound to BRD-7880

Abdul Azeez, K.R., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 41.06 kDa
Atom Count: 3,166
Modeled Residue Count: 338
Deposited Residue Count: 344
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase C	A	274	Homo sapiens	Mutation(s): 0 Gene Names: AURKC, AIE2, AIK3, AIRK3, ARK3, STK13 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQB9 (Homo sapiens) Explore Q9UQB9 Go to UniProtKB: Q9UQB9
PHAROS: Q9UQB9 GTEx: ENSG00000105146
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UQB9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner centromere protein	B	70	Homo sapiens	Mutation(s): 0 Gene Names: INCENP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS7 (Homo sapiens) Explore Q9NQS7 Go to UniProtKB: Q9NQS7
PHAROS: Q9NQS7 GTEx: ENSG00000149503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NQS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F8Z Query on F8Z 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]	1-[(2~{R},3~{S})-2-[[1,3-benzodioxol-5-ylmethyl(methyl)amino]methyl]-3-methyl-6-oxidanylidene-5-[(2~{S})-1-oxidanylpropan-2-yl]-3,4-dihydro-2~{H}-1,5-benzoxazocin-8-yl]-3-(4-methoxyphenyl)urea C₃₂ H₃₈ N₄ O₇ NGRSXEMLDRQNMH-LPBFERMMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SEP Query on SEP	B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.216 (Depositor), 0.230 (DCC)
R-Value Work: 0.176 (Depositor), 0.190 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.65	α = 90
b = 72.48	β = 90
c = 83.06	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary