3ZBY

Ligand-free structure of CYP142 from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb3ZBY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2012-11-13 Released: 2013-02-27
Deposition Author(s): Garcia-Fernandez, E., Frank, D.J., Galan, B., Kells, P.M., Podust, L.M., Garcia, J.L., Ortiz de Montellano, P.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.230
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 287.3 kDa
Atom Count: 22,588
Modelled Residue Count: 2,414
Deposited Residue Count: 2,442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P450 HEME-THIOLATE PROTEIN	A, B, C, D, E A, B, C, D, E, F	407	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0R4Q6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R4Q6 Go to UniProtKB: A0R4Q6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R4Q6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	G, H, I, J, K G, H, I, J, K, L	7		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G01435GL GlyCosmos: G01435GL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain KA [auth F] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C]	AA [auth D] FA [auth E] KA [auth F] M [auth A] Q [auth B] AA [auth D], FA [auth E], KA [auth F], M [auth A], Q [auth B], V [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain KA [auth F] Focus chain M [auth A] Focus chain Q [auth B] Focus chain V [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain LA [auth F] SDF format, chain MA [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	BA [auth D] CA [auth D] DA [auth D] GA [auth E] HA [auth E] BA [auth D], CA [auth D], DA [auth D], GA [auth E], HA [auth E], IA [auth E], LA [auth F], MA [auth F], N [auth A], NA [auth F], O [auth A], R [auth B], S [auth B], T [auth B], W [auth C], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain JA [auth E] SDF format, chain OA [auth F] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain Z [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth C]	EA [auth D] JA [auth E] OA [auth F] P [auth A] U [auth B] EA [auth D], JA [auth E], OA [auth F], P [auth A], U [auth B], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain JA [auth E] Focus chain OA [auth F] Focus chain P [auth A] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth D] Focus chain JA [auth E] Focus chain OA [auth F] Focus chain P [auth A] Focus chain U [auth B] Focus chain Z [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012 Query on PRD_900012	G, H, I, J, K G, H, I, J, K, L	beta-cyclodextrin	Oligosaccharide / Drug delivery		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.230
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.051	α = 90
b = 162.847	β = 90
c = 266.443	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

Ortiz de Montellano, P.R.

Revision History (Full details and data files)

Version 1.0: 2013-02-27
Type: Initial release
Version 1.1: 2013-05-01
Changes: Database references
Version 1.2: 2013-08-14
Changes: Database references
Version 1.3: 2018-02-07
Changes: Database references, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary