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), 0.250 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 EA [auth G] 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] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] 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] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] 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]	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]