5EHD | pdb_00005ehd

Crystal structure of human nucleophosmin-core in complex with cytochrome c

PDB DOI: https://doi.org/10.2210/pdb5EHD/pdb

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

Deposited: 2015-10-28 Released: 2016-11-09
Deposition Author(s): Bernardo-Garcia, N., Hermoso, J.A., Gonzalez-Arzola, K., Diaz-Moreno, I., De la Rosa, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.229 (Depositor), 0.159 (DCC)
R-Value Work:
0.164 (Depositor), 0.161 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human nucleophosmin-core in complex with cytochrome c

Bernardo-Garcia, N., Hermoso, J.A., Gonzalez-Arzola, K., Diaz-Moreno, I., De la Rosa, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 253.61 kDa
Atom Count: 16,452
Modeled Residue Count: 2,125
Deposited Residue Count: 2,320
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleophosmin	A B C D E A, B, C, D, E, F, G, H, I, J, K [auth a], L [auth b], M [auth c], N [auth d], O [auth e], P [auth f], Q [auth g], R [auth h], S [auth i], T [auth j]	116	Homo sapiens	Mutation(s): 0 Gene Names: NPM1, NPM
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens) Explore P06748 Go to UniProtKB: P06748
PHAROS: P06748 GTEx: ENSG00000181163
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06748
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth G] SDF format, chain W [auth b] SDF format, chain X [auth f] MOL2 format, chain U [auth A] MOL2 format, chain V [auth G] MOL2 format, chain W [auth b] MOL2 format, chain X [auth f] mmCIF format, chain U [auth A] mmCIF format, chain V [auth G] mmCIF format, chain W [auth b] mmCIF format, chain X [auth f]	U [auth A], V [auth G], W [auth b], X [auth f]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain U [auth A] Focus chain V [auth G] Focus chain W [auth b] Focus chain X [auth f] Interactions & Density Focus chain U [auth A] Focus chain V [auth G] Focus chain W [auth b] Focus chain X [auth f]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.229 (Depositor), 0.159 (DCC)
R-Value Work: 0.164 (Depositor), 0.161 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.799	α = 90
b = 179.72	β = 94.32
c = 104.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-11-09

Deposition Author(s):

Bernardo-Garcia, N.

Gonzalez-Arzola, K.

Diaz-Moreno, I.

De la Rosa, M.A.

Revision History (Full details and data files)

Version 1.0: 2016-11-09
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.