7CX8 | pdb_00007cx8

Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Tetralylamine

PDB DOI: https://doi.org/10.2210/pdb7CX8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-09-01 Released: 2021-09-08
Deposition Author(s): Stanfield, J.K., Sugimoto, H., Shoji, O.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Tetralylamine at 1.70 Angstrom Resolution

Shoji, O., Stanfield, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 108.47 kDa
Atom Count: 8,442
Modeled Residue Count: 910
Deposited Residue Count: 912
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	456	Priestia megaterium	Mutation(s): 0 Gene Names: cyp102A1 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain C [auth A]	C [auth A], O [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
GKX (Subject of Investigation/LOI) Query on GKX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B]	D [auth A], P [auth B]	(2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid C₂₀ H₂₉ N O₃ HMRCCMCZAAWOCJ-SFHVURJKSA-N		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
STQ Query on STQ Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B]	F [auth A], R [auth B]	(1~{S})-1,2,3,4-tetrahydronaphthalen-1-amine C₁₀ H₁₃ N JRZGPXSSNPTNMA-JTQLQIEISA-N		Interactions Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain R [auth B]
1Y5 (Subject of Investigation/LOI) Query on 1Y5 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth B]	E [auth A], Q [auth B]	(1R)-1,2,3,4-tetrahydronaphthalen-1-amine C₁₀ H₁₃ N JRZGPXSSNPTNMA-SNVBAGLBSA-N		Interactions Focus chain E [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain Q [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain M [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] 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] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] 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] Focus chain X [auth B] Focus chain Y [auth B]