5T8S | pdb_00005t8s

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

PDB DOI: https://doi.org/10.2210/pdb5T8S/pdb

Classification: TRANSFERASE
Organism(s): Neisseria gonorrhoeae FA 1090
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-08 Released: 2016-09-28
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.171 (Depositor), 0.170 (DCC)
R-Value Work:
0.148 (Depositor), 0.149 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
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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 a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

Dranow, D.M., Delker, S.L., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 87.41 kDa
Atom Count: 6,639
Modeled Residue Count: 764
Deposited Residue Count: 794
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase	A, B	397	Neisseria gonorrhoeae FA 1090	Mutation(s): 0 Gene Names: metK, NGO0106 EC: 2.5.1.6
UniProt
Find proteins for Q5FAC0 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5FAC0 Go to UniProtKB: Q5FAC0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FAC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
3PO Query on 3PO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	TRIPHOSPHATE H₅ O₁₀ P₃ UNXRWKVEANCORM-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	C [auth A], E [auth A], H [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.171 (Depositor), 0.170 (DCC)
R-Value Work: 0.148 (Depositor), 0.149 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.71	α = 90
b = 115.71	β = 90
c = 146.24	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MR-Rosetta	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-10-22
Changes: Structure summary

5T8S | pdb_00005t8s

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

Literature

Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)