7DT0 | pdb_00007dt0

Proline hydroxylase H11-N101I mutant

PDB DOI: https://doi.org/10.2210/pdb7DT0/pdb

Classification: HYDROLASE
Organism(s): uncultured bacterium esnapd13
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-04 Released: 2022-01-12
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: 2.43 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.201 (Depositor), 0.207 (DCC)
R-Value Observed:
0.204 (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

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: 241.47 kDa
Atom Count: 15,768
Modeled Residue Count: 1,958
Deposited Residue Count: 2,128
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, C, D, E A, B, C, D, E, F, G, H	266	uncultured bacterium esnapd13	Mutation(s): 1
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 3 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 AA [auth G] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain DA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain DA [auth H] mmCIF format, chain AA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain DA [auth H]	AA [auth G] DA [auth H] I [auth A] L [auth B] O [auth C] AA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
PRO (Subject of Investigation/LOI) Query on PRO Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	CA [auth G] FA [auth H] K [auth A] M [auth B] Q [auth C] CA [auth G], FA [auth H], K [auth A], M [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth F]	BA [auth G] EA [auth H] J [auth A] N [auth B] P [auth C] BA [auth G], EA [auth H], J [auth A], N [auth B], P [auth C], S [auth D], V [auth E], Y [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Y [auth F]