2C9Y

Structure of human adenylate kinase 2

PDB DOI: https://doi.org/10.2210/pdb2C9Y/pdb

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

Deposited: 2005-12-15 Released: 2006-01-04
Deposition Author(s): Bunkoczi, G., Filippakopoulos, P., Debreczeni, J.E., Turnbull, A., Papagrigoriou, E., Savitsky, P., Colebrook, S., von Delft, F., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.274 (Depositor), 0.280 (DCC)
R-Value Work:
0.194 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Human Adenylate Kinase 2

Bunkoczi, G., Filippakopoulos, P., Debreczeni, J.E., Turnbull, A., Papagrigoriou, E., Savitsky, P., Colebrook, S., von Delft, F., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 27.81 kDa
Atom Count: 1,938
Modelled Residue Count: 218
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLATE KINASE ISOENZYME 2, MITOCHONDRIAL	A	242	Homo sapiens	Mutation(s): 0 EC: 2.7.4.3
UniProt & NIH Common Fund Data Resources
Find proteins for P54819 (Homo sapiens) Explore P54819 Go to UniProtKB: P54819
PHAROS: P54819 GTEx: ENSG00000004455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54819
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B4P Query on B4P Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	BIS(ADENOSINE)-5'-TETRAPHOSPHATE C₂₀ H₂₈ N₁₀ O₁₉ P₄ YOAHKNVSNCMZGQ-XPWFQUROSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.274 (Depositor), 0.280 (DCC)
R-Value Work: 0.194 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.042	α = 90
b = 49.26	β = 90
c = 127.001	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-01-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-01-04
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: 2018-02-28
Changes: Source and taxonomy
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description
Version 1.5: 2024-10-23
Changes: Structure summary