3QVE | pdb_00003qve

Crystal structure of human HMG box-containing protein 1, HBP1

PDB DOI: https://doi.org/10.2210/pdb3QVE/pdb

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

Deposited: 2011-02-25 Released: 2011-03-16
Deposition Author(s): Chaikuad, A., Krysztofinska, E., Cocking, R., Vollmar, M., Yue, W.W., Krojer, T., Ugochukwu, E., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human HMG box-containing protein 1, HBP1

Chaikuad, A., Krysztofinska, E., Cocking, R., Vollmar, M., Yue, W.W., Krojer, T., Ugochukwu, E., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Bountra, C., Oppermann, U., Structural Genomics Consortium

To be published.

Macromolecule Content

Total Structure Weight: 48.93 kDa
Atom Count: 3,603
Modelled Residue Count: 389
Deposited Residue Count: 417
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMG box-containing protein 1	A, B, C	139	Homo sapiens	Mutation(s): 0 Gene Names: HBP1
UniProt & NIH Common Fund Data Resources
Find proteins for O60381 (Homo sapiens) Explore O60381 Go to UniProtKB: O60381
PHAROS: O60381 GTEx: ENSG00000105856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60381
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain Q [auth B] SDF format, chain D [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain D [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain D [auth A]	D [auth A], HA [auth C], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain HA [auth C] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain HA [auth C] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain DA [auth B] SDF format, chain MA [auth C] SDF format, chain X [auth B] SDF format, chain Z [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] 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 AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.84	α = 90
b = 118.84	β = 90
c = 93.19	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-03-16

Deposition Author(s):

Structural Genomics Consortium

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-03-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description