8DMG

CYP102A1 in Closed Conformation

PDB DOI: https://doi.org/10.2210/pdb8DMG/pdb
EM Map EMD-27536: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-08 Released: 2023-07-19
Deposition Author(s): Su, M., Xu, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM

Su, M., Xu, H.

To be published.

Macromolecule Content

Total Structure Weight: 239.5 kDa
Atom Count: 16,642
Modelled Residue Count: 2,068
Deposited Residue Count: 2,074
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	1,037	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 0
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B]	F [auth A], O [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B]	C [auth A], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B]	E [auth A], N [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
1C6 Query on 1C6 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B]	D [auth A], M [auth B]	6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole C₁₇ H₁₉ N₃ O₂ S XURCIPRUUASYLR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
PG4 (Subject of Investigation/LOI) Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	J [auth A], K [auth A], S [auth B], T [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	G [auth A] H [auth A] I [auth A] P [auth B] Q [auth B] G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]