9JG7 | pdb_00009jg7

Artificial serine-dependent beta-lactamase, S2

PDB DOI: https://doi.org/10.2210/pdb9JG7/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-06 Released: 2025-09-10
Deposition Author(s): Song, W.J., Yu, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.231 (Depositor), 0.233 (DCC)
R-Value Work:
0.184 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Chemical crossover between metallo- and serine-dependent beta-lactamases

Song, W.J., Yu, J.

To be published.

Macromolecule Content

Total Structure Weight: 102.23 kDa
Atom Count: 7,591
Modeled Residue Count: 848
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
artificial serine-dependent beta-lactamase	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth M], H [auth O]	106	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain FA [auth K] SDF format, chain I [auth A] SDF format, chain JA [auth M] SDF format, chain O [auth C] SDF format, chain OA [auth O] SDF format, chain S [auth E] SDF format, chain W [auth G] SDF format, chain BA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth M] MOL2 format, chain O [auth C] MOL2 format, chain OA [auth O] MOL2 format, chain S [auth E] MOL2 format, chain W [auth G] MOL2 format, chain BA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth M] mmCIF format, chain O [auth C] mmCIF format, chain OA [auth O] mmCIF format, chain S [auth E] mmCIF format, chain W [auth G] mmCIF format, chain BA [auth I]	BA [auth I] FA [auth K] I [auth A] JA [auth M] O [auth C] BA [auth I], FA [auth K], I [auth A], JA [auth M], O [auth C], OA [auth O], S [auth E], W [auth G]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain BA [auth I] Focus chain FA [auth K] Focus chain I [auth A] Focus chain JA [auth M] Focus chain O [auth C] Focus chain OA [auth O] Focus chain S [auth E] Focus chain W [auth G] Interactions & Density Focus chain BA [auth I] Focus chain FA [auth K] Focus chain I [auth A] Focus chain JA [auth M] Focus chain O [auth C] Focus chain OA [auth O] Focus chain S [auth E] Focus chain W [auth G]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain EA [auth I] SDF format, chain Q [auth C] SDF format, chain N [auth A] MOL2 format, chain EA [auth I] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth A] mmCIF format, chain EA [auth I] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth A]	EA [auth I], N [auth A], Q [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain EA [auth I] Focus chain N [auth A] Focus chain Q [auth C] Interactions & Density Focus chain EA [auth I] Focus chain N [auth A] Focus chain Q [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth I] SDF format, chain HA [auth K] SDF format, chain IA [auth K] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth M] SDF format, chain NA [auth M] SDF format, chain QA [auth O] SDF format, chain R [auth C] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain Y [auth G] SDF format, chain Z [auth G] SDF format, chain LA [auth M] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth I] MOL2 format, chain HA [auth K] MOL2 format, chain IA [auth K] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth M] MOL2 format, chain NA [auth M] MOL2 format, chain QA [auth O] MOL2 format, chain R [auth C] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain LA [auth M] mmCIF format, chain AA [auth G] mmCIF format, chain DA [auth I] mmCIF format, chain HA [auth K] mmCIF format, chain IA [auth K] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth M] mmCIF format, chain NA [auth M] mmCIF format, chain QA [auth O] mmCIF format, chain R [auth C] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain LA [auth M]	AA [auth G] DA [auth I] HA [auth K] IA [auth K] K [auth A] AA [auth G], DA [auth I], HA [auth K], IA [auth K], K [auth A], L [auth A], LA [auth M], M [auth A], MA [auth M], NA [auth M], QA [auth O], R [auth C], U [auth E], V [auth E], Y [auth G], Z [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth I] Focus chain HA [auth K] Focus chain IA [auth K] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth M] Focus chain M [auth A] Focus chain MA [auth M] Focus chain NA [auth M] Focus chain QA [auth O] Focus chain R [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth I] Focus chain HA [auth K] Focus chain IA [auth K] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth M] Focus chain M [auth A] Focus chain MA [auth M] Focus chain NA [auth M] Focus chain QA [auth O] Focus chain R [auth C] Focus chain U [auth E] Focus chain V [auth E] Focus chain Y [auth G] Focus chain Z [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain GA [auth K] SDF format, chain J [auth A] SDF format, chain KA [auth M] SDF format, chain P [auth C] SDF format, chain PA [auth O] SDF format, chain T [auth E] SDF format, chain X [auth G] MOL2 format, chain CA [auth I] MOL2 format, chain GA [auth K] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth M] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth O] MOL2 format, chain T [auth E] MOL2 format, chain X [auth G] mmCIF format, chain CA [auth I] mmCIF format, chain GA [auth K] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth M] mmCIF format, chain P [auth C] mmCIF format, chain PA [auth O] mmCIF format, chain T [auth E] mmCIF format, chain X [auth G]	CA [auth I] GA [auth K] J [auth A] KA [auth M] P [auth C] CA [auth I], GA [auth K], J [auth A], KA [auth M], P [auth C], PA [auth O], T [auth E], X [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth I] Focus chain GA [auth K] Focus chain J [auth A] Focus chain KA [auth M] Focus chain P [auth C] Focus chain PA [auth O] Focus chain T [auth E] Focus chain X [auth G] Interactions & Density Focus chain CA [auth I] Focus chain GA [auth K] Focus chain J [auth A] Focus chain KA [auth M] Focus chain P [auth C] Focus chain PA [auth O] Focus chain T [auth E] Focus chain X [auth G]