7CP8 | pdb_00007cp8

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

PDB DOI: https://doi.org/10.2210/pdb7CP8/pdb

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

Deposited: 2020-08-06 Released: 2021-09-15
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: 1.68 Å
R-Value Free:
0.213 (Depositor), 0.218 (DCC)
R-Value Work:
0.183 (Depositor), 0.192 (DCC)
R-Value Observed:
0.184 (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

Structure of the CYP102A1 Haem Domain with N-(5-Cyclohexyl)valeroyl-L-Phenylalanine in complex with (R)-1-Indanylamine at 1.68 Angstrom Resolution

Shoji, O., Stanfield, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 108.73 kDa
Atom Count: 8,639
Modeled Residue Count: 908
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain X [auth B]	C [auth A], X [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain X [auth B]
GKX (Subject of Investigation/LOI) Query on GKX Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain E [auth A]	E [auth A], Z [auth B]	(2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid C₂₀ H₂₉ N O₃ HMRCCMCZAAWOCJ-SFHVURJKSA-N		Interactions Focus chain E [auth A] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain Z [auth B]
RM1 (Subject of Investigation/LOI) Query on RM1 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain D [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain D [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain D [auth A]	D [auth A], Y [auth B]	N-METHYL-1(R)-AMINOINDAN C₁₀ H₁₃ N AIXUYZODYPPNAV-SNVBAGLBSA-N		Interactions Focus chain D [auth A] Focus chain Y [auth B] Interactions & Density Focus chain D [auth A] Focus chain Y [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] 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 S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] 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 S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A] 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 S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] CA [auth B] F [auth A] G [auth A] AA [auth B], BA [auth B], CA [auth B], F [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], O [auth A], P [auth B], Q [auth B], 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 AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] 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 O [auth A] Focus chain P [auth B] Focus chain Q [auth B] 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 AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain F [auth A] 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 O [auth A] Focus chain P [auth B] Focus chain Q [auth B] 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]