7E00 | pdb_00007e00

Trans-proline-hydroxylase H11 with Succinic and L-proline in the fourth reaction state.

PDB DOI: https://doi.org/10.2210/pdb7E00/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium esnapd13
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-01-26 Released: 2022-02-02
Deposition Author(s): Gong, W.G., Yang, L.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.230 (Depositor), 0.241 (DCC)
R-Value Work:
0.195 (Depositor), 0.207 (DCC)

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

Trans-3/4-proline-hydroxylase H11 with AKG and L-proline

Gong, W.G., Yang, L.Y.

To be published.

Macromolecule Content

Total Structure Weight: 60.85 kDa
Atom Count: 4,452
Modeled Residue Count: 530
Deposited Residue Count: 536
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytanoyl-CoA dioxygenase	A, B	268	uncultured bacterium esnapd13	Mutation(s): 0
UniProt
Find proteins for S5TUM1 (uncultured bacterium esnapd13) Explore S5TUM1 Go to UniProtKB: S5TUM1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S5TUM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG (Subject of Investigation/LOI) Query on AKG 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]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
SIN (Subject of Investigation/LOI) Query on SIN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
PRO (Subject of Investigation/LOI) Query on PRO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
O (Subject of Investigation/LOI) Query on O Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]