7Z79 | pdb_00007z79

Crystal structure of aminotransferase-like protein from Variovorax paradoxus

PDB DOI: https://doi.org/10.2210/pdb7Z79/pdb

Classification: TRANSFERASE
Organism(s): Variovorax paradoxus B4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-15 Released: 2022-04-13
Deposition Author(s): Boyko, K.M., Matyuta, I.O., Nikolaeva, A.Y., Khrenova, M.G., Rakitina, T.V., Popov, V.O., Bezsudnova, E.Y.
Funding Organization(s): Ministry of Science and Higher Education of the Russian Federation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.229 (DCC)
R-Value Work:
0.205 (Depositor), 0.207 (DCC)
R-Value Observed:
0.207 (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

A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine

Boyko, K.M., Matyuta, I.O., Nikolaeva, A.Y., Rakitina, T.V., Popov, V.O., Bezsudnova, E.Y., Khrenova, M.G.

(2022) Crystals (Basel) 12

DOI: https://doi.org/10.3390/cryst12050619

Macromolecule Content

Total Structure Weight: 207.1 kDa
Atom Count: 14,415
Modeled Residue Count: 1,793
Deposited Residue Count: 1,902
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class 4	A, B, C, D, E A, B, C, D, E, F	317	Variovorax paradoxus B4	Mutation(s): 0 Gene Names: VAPA_1c54540 EC: 2.6.1.42
UniProt
Find proteins for T1XIY1 (Variovorax paradoxus B4) Explore T1XIY1 Go to UniProtKB: T1XIY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T1XIY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth F] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D]	AA [auth E] FA [auth F] I [auth A] O [auth B] R [auth C] AA [auth E], FA [auth F], I [auth A], O [auth B], R [auth C], U [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain I [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E]	EA [auth F] L [auth B] M [auth B] N [auth B] X [auth E] EA [auth F], L [auth B], M [auth B], N [auth B], X [auth E], Y [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain X [auth E] Focus chain Y [auth E] Interactions & Density Focus chain EA [auth F] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain X [auth E] Focus chain Y [auth E]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain GA [auth F] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	BA [auth E] GA [auth F] J [auth A] P [auth B] S [auth C] BA [auth E], GA [auth F], J [auth A], P [auth B], S [auth C], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain J [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth E]	CA [auth E] DA [auth F] G [auth A] H [auth A] K [auth A] CA [auth E], DA [auth F], G [auth A], H [auth A], K [auth A], Q [auth C], T [auth D], W [auth E], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth E]