3TLX | pdb_00003tlx

Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum

PDB DOI: https://doi.org/10.2210/pdb3TLX/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium falciparum
Mutation(s): No

Deposited: 2011-08-30 Released: 2011-10-26
Deposition Author(s): Wernimont, A.K., Loppnau, P., Crombet, L., Weadge, J., Perieteanu, A., Edwards, A.M., Arrowsmith, C.H., Park, H., Bountra, C., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.260 (Depositor), 0.290 (DCC)
R-Value Work:
0.226 (Depositor), 0.240 (DCC)
R-Value Observed:
0.227 (Depositor)

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 PF10_0086, adenylate kinase from plasmodium falciparum

Wernimont, A.K., Loppnau, P., Crombet, L., Weadge, J., Perieteanu, A., Edwards, A.M., Arrowsmith, C.H., Park, H., Bountra, C., Hui, R., Amani, M.

To be published.

Macromolecule Content

Total Structure Weight: 113.03 kDa
Atom Count: 5,817
Modeled Residue Count: 812
Deposited Residue Count: 972
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 2	A, B, C, D	243	Plasmodium falciparum	Mutation(s): 0 EC: 2.7.4.3
UniProt
Find proteins for Q8IJV6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJV6 Go to UniProtKB: Q8IJV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IJV6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	H [auth A], I [auth B], J [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.260 (Depositor), 0.290 (DCC)
R-Value Work: 0.226 (Depositor), 0.240 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.395	α = 90
b = 76.663	β = 100.78
c = 93.768	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2014-11-12
Changes: Structure summary
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 3TLX | pdb_00003tlx

Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum

Crystal Structure of PF10_0086, adenylate kinase from plasmodium falciparum

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3TLX | pdb_00003tlx