5K7X

Fully ligated Adenylosuccinate Synthetase from Pyrococcus horikoshii OT3 with GTP, IMP and Hadacidin

PDB DOI: https://doi.org/10.2210/pdb5K7X/pdb

Classification: LIGASE
Organism(s): Pyrococcus horikoshii OT3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-27 Released: 2016-12-07
Deposition Author(s): Xie, Y., Cheng, Z.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.263
R-Value Work: 0.206
R-Value Observed: 0.209

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of hypothetical adenylosuccinate synthetase, PH0438 from Pyrococcus horikoshii OT3

Xie, Y., Kishisita, S., Murayama, K., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 230.6 kDa
Atom Count: 16,066
Modelled Residue Count: 2,022
Deposited Residue Count: 2,040
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	A, B, C, D, E A, B, C, D, E, F	340	Pyrococcus horikoshii OT3	Mutation(s): 0 Gene Names: purA, PH0438 EC: 6.3.4.4
UniProt
Find proteins for O58187 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58187 Go to UniProtKB: O58187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O58187
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E]	AA [auth F] G [auth A] K [auth B] O [auth C] S [auth D] AA [auth F], G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain W [auth E]
IMP Query on IMP Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E]	BA [auth F] H [auth A] L [auth B] P [auth C] T [auth D] BA [auth F], H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	INOSINIC ACID C₁₀ H₁₃ N₄ O₈ P GRSZFWQUAKGDAV-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
HDA Query on HDA Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Y [auth E]	CA [auth F] I [auth A] M [auth B] Q [auth C] U [auth D] CA [auth F], I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	HADACIDIN C₃ H₅ N O₄ URJHVPKUWOUENU-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	DA [auth F] J [auth A] N [auth B] R [auth C] V [auth D] DA [auth F], J [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.263
R-Value Work: 0.206
R-Value Observed: 0.209
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.348	α = 90
b = 130.549	β = 90
c = 168.673	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Xie, Y.

Cheng, Z.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81473114

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2017-08-16
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description