8GOG | pdb_00008gog

Structure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))

PDB DOI: https://doi.org/10.2210/pdb8GOG/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-08-24 Released: 2024-02-28
Deposition Author(s): Sairaman, A., Mukherjee, P., Maiti, D., Bhaumik, P.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.294 (Depositor), 0.294 (DCC)
R-Value Work:
0.251 (Depositor), 0.251 (DCC)
R-Value Observed:
0.253 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Enantiodivergent synthesis of isoindolones catalysed by a Rh(III)-based artificial metalloenzyme

Mukherjee, P., Sairaman, A., Deka, H.J., Jain, S., Mishra, S.K., Roy, S., Bhaumik, P., Maiti, D.

(2024) Nat Synth 3: 835-845

DOI: https://doi.org/10.1038/s44160-024-00533-5

Macromolecule Content

Total Structure Weight: 28.78 kDa
Atom Count: 2,064
Modeled Residue Count: 242
Deposited Residue Count: 242
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B	121	Streptomyces avidinii	Mutation(s): 2
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JSU (Subject of Investigation/LOI) Query on JSU Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain D [auth A]	D [auth A], P [auth B]	trichloro((3~{a}~{S},4~{S},6~{a}~{R})-4-[(5~{R})-5-oxidanyl-5-[2-(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-ylidene)ethylamino]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-one)rhodium(3+) C₂₁ H₃₂ Cl₃ N₃ O₂ Rh S VZIPCMCWYKDVTP-PCIMLXTCSA-K		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
RH3 Query on RH3 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], N [auth B], O [auth B]	RHODIUM(III) ION Rh PZSJYEAHAINDJI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	F [auth A] J [auth A] K [auth A] R [auth B] S [auth B] F [auth A], J [auth A], K [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B]