7HK8 | pdb_00007hk8

Crystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione, C2221 form

PDB DOI: https://doi.org/10.2210/pdb7HK8/pdb
Deposition Group: G_1002306 | Explore G_1002306

Classification: HYDROLASE
Organism(s): Glutamicibacter protophormiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-10 Released: 2026-04-15
Deposition Author(s): Stihle, M., Benz, J., Asztalos, P., Rudolph, M.G.
Funding Organization(s): F. Hoffmann-La Roche LTD

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.231 (Depositor), 0.237 (DCC)
R-Value Work:
0.192 (Depositor), 0.198 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7HK8

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of a N-methylhydantoinase complex

Asztalos, P., Meier, T., Clairfeuille, T., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 285.61 kDa
Atom Count: 19,901
Modeled Residue Count: 2,564
Deposited Residue Count: 2,576
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-methylhydantoinase	A, B	1,288	Glutamicibacter protophormiae	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	DA [auth B] EA [auth B] F [auth A] FA [auth B] G [auth A] DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A]
A1BC1 (Subject of Investigation/LOI) Query on A1BC1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain BA [auth B]	BA [auth B], D [auth A]	1-methylimidazolidine-2,4-dione C₄ H₆ N₂ O₂ RHYBFKMFHLPQPH-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain D [auth A] Interactions & Density Focus chain BA [auth B] Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain Z [auth A] SDF format, chain YA [auth B] SDF format, chain Y [auth A] SDF format, chain XA [auth B] SDF format, chain X [auth A] SDF format, chain WA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain V [auth A] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] J [auth A] JA [auth B] K [auth A] HA [auth B], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain HA [auth B] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain AA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain AA [auth B]	AA [auth B], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain C [auth A] Interactions & Density Focus chain AA [auth B] Focus chain C [auth A]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain CA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B]	CA [auth B], E [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain CA [auth B] Focus chain E [auth A] Interactions & Density Focus chain CA [auth B] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.231 (Depositor), 0.237 (DCC)
R-Value Work: 0.192 (Depositor), 0.198 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.41	α = 90
b = 265.92	β = 90
c = 120.81	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
F. Hoffmann-La Roche LTD	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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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.