7UOR | pdb_00007uor

Crystal structure of cytochrome P450 enzyme CYP119 in complex with methyliridium(III) mesoporphyrin.

PDB DOI: https://doi.org/10.2210/pdb7UOR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sulfolobus acidocaldarius
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-04-13 Released: 2023-02-22
Deposition Author(s): Pereira, J.H., Bloomer, B.J., Hartwig, J.F., Adams, P.D.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free:
0.229 (Depositor), 0.224 (DCC)
R-Value Work:
0.181 (Depositor), 0.178 (DCC)
R-Value Observed:
0.183 (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

Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics

Bloomer, B.J., Natoli, S.N., Garcia-Borras, M., Pereira, J.H., Hu, D.B., Adams, P.D., Houk, K.N., Clark, D.S., Hartwig, J.F.

(2023) Nat Catal 6: 39-51

DOI: https://doi.org/10.1038/s41929-022-00899-9

Macromolecule Content

Total Structure Weight: 276.35 kDa
Atom Count: 19,154
Modeled Residue Count: 2,274
Deposited Residue Count: 2,310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome	A, B, C, D, E A, B, C, D, E, F	385	Sulfolobus acidocaldarius	Mutation(s): 4 Gene Names: ATY89_07675, ATZ20_10695 EC: 1.14 (UniProt), 1.11.1.7 (UniProt)
UniProt
Find proteins for Q55080 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q55080 Go to UniProtKB: Q55080
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q55080
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HIR (Subject of Investigation/LOI) Query on HIR Download:Ideal Coordinates CCD File SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] L [auth C] N [auth D] Q [auth E] G [auth A], J [auth B], L [auth C], N [auth D], Q [auth E], S [auth F]	methyliridium(III) mesoporphyrin C₃₅ H₃₃ Ir N₄ O₅ SMNGZJSFEBZLGV-HXFTUNQESA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] M [auth C] O [auth D] R [auth E] H [auth A], K [auth B], M [auth C], O [auth D], R [auth E], T [auth F]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain I [auth A] MOL2 format, chain P [auth D] MOL2 format, chain I [auth A] mmCIF format, chain P [auth D] mmCIF format, chain I [auth A]	I [auth A], P [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth D] Interactions & Density Focus chain I [auth A] Focus chain P [auth D]