6PJW | pdb_00006pjw

Adenylate kinase from Methanococcus igneus - AMP bound form

PDB DOI: https://doi.org/10.2210/pdb6PJW/pdb

Classification: TRANSFERASE
Organism(s): Methanotorris igneus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-06-28 Released: 2020-01-22
Deposition Author(s): Moon, S., Kim, J., Olmos, J.L., 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: 2.40 Å
R-Value Free:
0.248 (Depositor), 0.254 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6PJW

Ligand Structure Quality Assessment

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

Literature

Adenylate kinase from Methanococcus igneus - AMP bound form

Bae, E.

To be published.

Macromolecule Content

Total Structure Weight: 278.64 kDa
Atom Count: 18,632
Modeled Residue Count: 2,292
Deposited Residue Count: 2,400
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain OA [auth J] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain QA [auth K] SDF format, chain RA [auth K] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain TA [auth L] SDF format, chain UA [auth L] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain EA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth L] MOL2 format, chain UA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain EA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth K] mmCIF format, chain RA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth L] mmCIF format, chain UA [auth L] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain EA [auth G]	BA [auth F] CA [auth F] EA [auth G] FA [auth G] HA [auth H] BA [auth F], CA [auth F], EA [auth G], FA [auth G], HA [auth H], IA [auth H], KA [auth I], LA [auth I], M [auth A], N [auth A], NA [auth J], OA [auth J], P [auth B], Q [auth B], QA [auth K], RA [auth K], S [auth C], T [auth C], TA [auth L], UA [auth L], V [auth D], W [auth D], Y [auth E], Z [auth E]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth L] Focus chain UA [auth L] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain P [auth B] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain RA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth L] Focus chain UA [auth L] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain JA [auth H] SDF format, chain MA [auth I] SDF format, chain O [auth A] SDF format, chain PA [auth J] SDF format, chain R [auth B] SDF format, chain SA [auth K] SDF format, chain U [auth C] SDF format, chain VA [auth L] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth L] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain VA [auth L] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] GA [auth G] JA [auth H] MA [auth I] AA [auth E], DA [auth F], GA [auth G], JA [auth H], MA [auth I], O [auth A], PA [auth J], R [auth B], SA [auth K], U [auth C], VA [auth L], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248 (Depositor), 0.254 (DCC)
R-Value Work: 0.200 (Depositor), 0.204 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.77	α = 90
b = 121.39	β = 102.95
c = 121.04	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-22

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: 2020-01-22
Type: Initial release
Version 1.1: 2020-09-23
Changes: Derived calculations, 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.