2BZK | pdb_00002bzk

CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND PIMTIDE

PDB DOI: https://doi.org/10.2210/pdb2BZK/pdb

Classification: TRANSFERASE/PEPTIDE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-08-18 Released: 2005-11-03
Deposition Author(s): Debreczeni, J.E., Bullock, A., Knapp, S., von Delft, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.225 (Depositor), 0.232 (DCC)
R-Value Work:
0.189 (Depositor), 0.197 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of the Human Pim1 in Complex with Amppnp and Pimtide

Debreczeni, J.E., Bullock, A., Knapp, S., von Delft, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.73 kDa
Atom Count: 2,277
Modeled Residue Count: 275
Deposited Residue Count: 328
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIMTIDE	A	15	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1	B	313	Homo sapiens	Mutation(s): 1 EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309 Go to UniProtKB: P11309
PHAROS: P11309 GTEx: ENSG00000137193
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11309
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.225 (Depositor), 0.232 (DCC)
R-Value Work: 0.189 (Depositor), 0.197 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.889	α = 90
b = 97.889	β = 90
c = 80.493	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-11-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2018-04-04
Changes: Data collection
Version 1.4: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description
Version 1.6: 2024-11-06
Changes: Structure summary