6G8R

SP140 PHD-Bromodomain complex with scFv

PDB DOI: https://doi.org/10.2210/pdb6G8R/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-09 Released: 2018-04-18
Deposition Author(s): Fairhead, M., Graslund, S., Strain-Damerell, C., Picaud, S.S., Pike, A.C.W., Pinkas, D.M., Wigren, E., Preger, C., Persson Lotsholm, H., Ossipova, E., Filippakopoulos, P., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.249
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

SP140 PHD-Bromodomain complex with scFv

Fairhead, M., Graslund, S., Strain-Damerell, C., Picaud, S.S., Pike, A.C.W., Pinkas, D.M., Wigren, E., Preger, C., Persson Lotsholm, H., Ossipova, E., Filippakopoulos, P., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 50.36 kDa
Atom Count: 3,063
Modelled Residue Count: 391
Deposited Residue Count: 448
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain variable fragment	A	250	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear body protein SP140	B	198	Homo sapiens	Mutation(s): 0 Gene Names: SP140, LYSP100
UniProt & NIH Common Fund Data Resources
Find proteins for Q13342 (Homo sapiens) Explore Q13342 Go to UniProtKB: Q13342
PHAROS: Q13342 GTEx: ENSG00000079263
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13342
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B]	E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.74 Å
R-Value Free: 0.249
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.2	α = 90
b = 89.2	β = 90
c = 343.35	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2019-01-16
Changes: Data collection, Derived calculations, Structure summary
Version 2.0: 2019-11-13
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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Help and Resources

6G8R

SP140 PHD-Bromodomain complex with scFv

SP140 PHD-Bromodomain complex with scFv

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)