2BBW | pdb_00002bbw

Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine pentaphosphate

PDB DOI: https://doi.org/10.2210/pdb2BBW/pdb

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

Deposited: 2005-10-17 Released: 2005-12-06
Deposition Author(s): Filippakopoulos, P., Turnbull, A.P., Fedorov, O., Weigelt, J., Bunkoczi, G., Ugochukwu, E., Debreczeni, J., Niesen, F., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.249 (Depositor), 0.247 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine pentaphosphate

Filippakopoulos, P., Turnbull, A.P., Fedorov, O., Weigelt, J., Bunkoczi, G., Ugochukwu, E., Debreczeni, J., Niesen, F., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 57.85 kDa
Atom Count: 3,720
Modeled Residue Count: 440
Deposited Residue Count: 492
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylate kinase 4, AK4	A, B	246	Homo sapiens	Mutation(s): 0 Gene Names: AK4 EC: 2.7.4.3 (PDB Primary Data), 2.7.4.4 (UniProt), 2.7.4.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27144 (Homo sapiens) Explore P27144 Go to UniProtKB: P27144
PHAROS: P27144 GTEx: ENSG00000162433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27144
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GP5 Query on GP5 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	DIGUANOSINE-PENTAPHOSPHATE C₂₀ H₂₉ N₁₀ O₂₄ P₅ RELSGTOCAPVUGP-DTFXMBEISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.249 (Depositor), 0.247 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.836	α = 90
b = 66.375	β = 91.5
c = 77.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	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: 2005-12-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-12-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description