Macromolecule Content

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

5EHD

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
R-Value Work: 0.164
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 1.0 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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06748
Protein Feature View 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]	U [auth A], V [auth G], W [auth b], X [auth f]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.229
R-Value Work: 0.164
R-Value Observed: 0.167
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

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.