6PK5 | pdb_00006pk5

Adenylate kinase from Methanococcus igneus - apo form

PDB DOI: https://doi.org/10.2210/pdb6PK5/pdb

Classification: TRANSFERASE
Organism(s): Methanotorris igneus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-28 Released: 2020-07-01
Deposition Author(s): Moon, S., Kim, J., Bae, E., Phillips Jr., G.N.
Funding Organization(s): National Research Foundation (NRF, Korea), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.267 (Depositor), 0.268 (DCC)
R-Value Work:
0.229 (Depositor), 0.231 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6PK5

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

Literature

Adenylate kinase from Methanococcus igneus - apo form

Bae, E.

To be published.

Macromolecule Content

Total Structure Weight: 135.54 kDa
Atom Count: 8,998
Modeled Residue Count: 1,137
Deposited Residue Count: 1,200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D, E A, B, C, D, E, F	200	Methanotorris igneus	Mutation(s): 0 Gene Names: adkA, adk EC: 2.7.4.3
UniProt
Find proteins for P43408 (Methanotorris igneus) Explore P43408 Go to UniProtKB: P43408
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43408
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth E], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.267 (Depositor), 0.268 (DCC)
R-Value Work: 0.229 (Depositor), 0.231 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.71	α = 90
b = 68.71	β = 90
c = 257.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Phillips Jr., G.N.

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	PJ013181
National Science Foundation (NSF, United States)	United States	1231306

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2020-09-23
Changes: Structure summary
Version 1.2: 2024-03-13
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.