7S5E | pdb_00007s5e

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS

PDB DOI: https://doi.org/10.2210/pdb7S5E/pdb

Classification: TRANSFERASE
Organism(s): Stenotrophomonas maltophilia K279a
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-10 Released: 2021-09-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.265 (Depositor), 0.264 (DCC)
R-Value Work:
0.226 (Depositor), 0.226 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279c with heterogeneous ligand states of GMP/ADP, GMP/-, GDP/-, and GMP/ATPgS.

Edwards, T.E., Horanyi, P.S., Abendroth, J., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 206.67 kDa
Atom Count: 12,787
Modeled Residue Count: 1,612
Deposited Residue Count: 1,832
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B, C, D, E A, B, C, D, E, F, G, H	229	Stenotrophomonas maltophilia K279a	Mutation(s): 0 Gene Names: gmk, Smlt3842 EC: 2.7.4.8
UniProt
Find proteins for B2FT06 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FT06 Go to UniProtKB: B2FT06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2FT06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain T [auth H] SDF format, chain N [auth D] MOL2 format, chain T [auth H] MOL2 format, chain N [auth D] mmCIF format, chain T [auth H] mmCIF format, chain N [auth D]	N [auth D], T [auth H]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain N [auth D] Focus chain T [auth H] Interactions & Density Focus chain N [auth D] Focus chain T [auth H]
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain R [auth G] SDF format, chain L [auth C] MOL2 format, chain R [auth G] MOL2 format, chain L [auth C] mmCIF format, chain R [auth G] mmCIF format, chain L [auth C]	L [auth C], R [auth G]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth C] Focus chain R [auth G] Interactions & Density Focus chain L [auth C] Focus chain R [auth G]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain J [auth A] MOL2 format, chain P [auth E] MOL2 format, chain J [auth A] mmCIF format, chain P [auth E] mmCIF format, chain J [auth A]	J [auth A], P [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain P [auth E] Interactions & Density Focus chain J [auth A] Focus chain P [auth E]
5GP (Subject of Investigation/LOI) Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain Q [auth F] SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth H] MOL2 format, chain Q [auth F] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth H] mmCIF format, chain Q [auth F] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth D] O [auth E] Q [auth F] I [auth A], K [auth B], M [auth D], O [auth E], Q [auth F], S [auth H]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain S [auth H]