7RST | pdb_00007rst

The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger

PDB DOI: https://doi.org/10.2210/pdb7RST/pdb

Classification: OXIDOREDUCTASE
Organism(s): Leptoxyphium fumago
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2021-08-11 Released: 2022-08-24
Deposition Author(s): Tang, X., Venkadesh, S., Zhou, J., Rosen, B., Wang, X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger

Tang, X., Venkadesh, S., Zhou, J., Rosen, B., Wang, X.

To be published.

Macromolecule Content

Total Structure Weight: 38.26 kDa
Atom Count: 3,113
Modeled Residue Count: 299
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloroperoxidase	A	299	Leptoxyphium fumago	Mutation(s): 0 Gene Names: CPO EC: 1.11.1.10
UniProt
Find proteins for P04963 (Leptoxyphium fumago) Explore P04963 Go to UniProtKB: P04963
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04963
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	D	2		O-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [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 A], Q [auth A], R [auth A], S [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions 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 A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density 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 A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain X [auth A] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain X [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain X [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] T [auth A] U [auth A] AA [auth A], BA [auth A], CA [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]