3NEY | pdb_00003ney

Crystal structure of the kinase domain of MPP1/p55

PDB DOI: https://doi.org/10.2210/pdb3NEY/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-06-09 Released: 2010-08-04
Deposition Author(s): Shen, Y., Tong, Y., Zhong, N., Guan, X., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.235 (Depositor), 0.234 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of the kinase domain of MPP1/p55

Shen, Y., Tong, Y., Zhong, N., Guan, X., Tempel, W., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 136.51 kDa
Atom Count: 8,713
Modeled Residue Count: 1,075
Deposited Residue Count: 1,182
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
55 kDa erythrocyte membrane protein	A B C D E [auth F] A, B, C, D, E [auth F], F [auth E]	197	Homo sapiens	Mutation(s): 0 Gene Names: MPP1, DXS552E, EMP55
UniProt & NIH Common Fund Data Resources
Find proteins for Q00013 (Homo sapiens) Explore Q00013 Go to UniProtKB: Q00013
PHAROS: Q00013 GTEx: ENSG00000130830
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00013
Sequence Annotations Expand
Reference Sequence

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 AA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain NA [auth F] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain Z [auth C] SDF format, chain Q [auth B] SDF format, chain HA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain HA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain HA [auth D]	AA [auth C] G [auth A] GA [auth D] H [auth A] HA [auth D] AA [auth C], G [auth A], GA [auth D], H [auth A], HA [auth D], NA [auth F], P [auth B], Q [auth B], R [auth B], S [auth B], SA [auth E], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth E] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain NA [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain SA [auth E] Focus chain Z [auth C]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain FA [auth C] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain N [auth A] SDF format, chain I [auth A] SDF format, chain EA [auth C] SDF format, chain DA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C]	BA [auth C] CA [auth C] DA [auth C] EA [auth C] FA [auth C] BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], O [auth A], OA [auth F], PA [auth F], QA [auth F], RA [auth F], T [auth B], TA [auth E], U [auth B], UA [auth E], V [auth B], VA [auth E], W [auth B], WA [auth E], X [auth B], Y [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain UA [auth E] Focus chain V [auth B] Focus chain VA [auth E] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.235 (Depositor), 0.234 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.088	α = 90
b = 131.562	β = 90
c = 237.19	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-11-12
Changes: Data collection
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary