1Z83 | pdb_00001z83

Crystal structure of human AK1A in complex with AP5A

PDB DOI: https://doi.org/10.2210/pdb1Z83/pdb

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

Deposited: 2005-03-29 Released: 2005-04-26
Deposition Author(s): Filippakopoulos, P., Bunkoczi, G., Jansson, A., Schreurs, A., Knapp, S., Edwards, A., von Delft, F., Sundstrom, M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.218 (Depositor), 0.225 (DCC)
R-Value Work:
0.169 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human AK1A in complex with AP5A

Filippakopoulos, P., Bunkoczi, G., Jansson, A., Schreurs, A., Knapp, S., Edwards, A., von Delft, F., Sundstrom, M.

To be published.

Macromolecule Content

Total Structure Weight: 69.07 kDa
Atom Count: 5,147
Modeled Residue Count: 585
Deposited Residue Count: 588
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase 1	A, B, C	196	Homo sapiens	Mutation(s): 0 Gene Names: AK1 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 P00568 (Homo sapiens) Explore P00568 Go to UniProtKB: P00568
PHAROS: P00568 GTEx: ENSG00000106992
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00568
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AP5 Query on AP5 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	G [auth A], M [auth B], Q [auth C]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C₂₀ H₂₉ N₁₀ O₂₂ P₅ OIMACDRJUANHTJ-XPWFQUROSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], K [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	D [auth A] E [auth A] H [auth B] I [auth B] J [auth B] D [auth A], E [auth A], H [auth B], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218 (Depositor), 0.225 (DCC)
R-Value Work: 0.169 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.194	α = 90
b = 46.259	β = 116.01
c = 119.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
EVAL15	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-04-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-04-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Database references, Structure summary
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description