2BWJ | pdb_00002bwj

Structure of adenylate kinase 5

PDB DOI: https://doi.org/10.2210/pdb2BWJ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-07-14 Released: 2005-07-21
Deposition Author(s): Bunkoczi, G., Filippakopoulos, P., Fedorov, O., Jansson, A., Longman, E., Ugochukwu, E., Knapp, S., von Delft, F., Arrowsmith, C., Edwards, A., Sundstrom, M., Weigelt, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of Adenylate Kinase 5

Filippakopoulos, P., Bunkoczi, G., Jansson, A., Longman, E., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 134.95 kDa
Atom Count: 9,288
Modeled Residue Count: 1,160
Deposited Residue Count: 1,194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLATE KINASE 5	A, B, C, D, E A, B, C, D, E, F	199	Homo sapiens	Mutation(s): 1 EC: 2.7.4.3 (PDB Primary Data), 2.7.4.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K8 (Homo sapiens) Explore Q9Y6K8 Go to UniProtKB: Q9Y6K8
PHAROS: Q9Y6K8 GTEx: ENSG00000154027
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6K8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain N [auth C] SDF format, chain L [auth B] MOL2 format, chain U [auth F] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] mmCIF format, chain U [auth F] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B]	L [auth B], N [auth C], U [auth F]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain L [auth B] Focus chain N [auth C] Focus chain U [auth F] Interactions & Density Focus chain L [auth B] Focus chain N [auth C] Focus chain U [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth B] M [auth C] O [auth D] G [auth A], H [auth A], J [auth B], M [auth C], O [auth D], P [auth E], R [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth E] Focus chain R [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A], K [auth B], Q [auth E], S [auth F], T [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.375	α = 90
b = 180.375	β = 90
c = 121.701	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-07-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2018-02-28
Changes: Source and taxonomy
Version 1.4: 2024-05-08
Changes: Data collection, Database references, Other