7QPR | pdb_00007qpr

Structure of full length SpoT

PDB DOI: https://doi.org/10.2210/pdb7QPR/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-01-05 Released: 2023-01-18
Deposition Author(s): Garcia-Pino, A., Tamman, H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.258 (Depositor), 0.216 (DCC)
R-Value Work:
0.221 (Depositor), 0.219 (DCC)
R-Value Observed:
0.223 (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

Structure of full length SpoT

Garcia-Pino, A., Tamman, H.

To be published.

Macromolecule Content

Total Structure Weight: 322.96 kDa
Atom Count: 22,585
Modeled Residue Count: 2,741
Deposited Residue Count: 2,804
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACT domain protein	A, B, C, D	701	Acinetobacter baumannii	Mutation(s): 0 Gene Names: spoT_1, relA_1, relA_3, spoT, A7M90_14410, AB945B12_01945, Aba9201_15290, ABCAM1_3401, ABKPCSM17A_01292, ABR2091_3374... spoT_1, relA_1, relA_3, spoT, A7M90_14410, AB945B12_01945, Aba9201_15290, ABCAM1_3401, ABKPCSM17A_01292, ABR2091_3374, ABUW_0309, APC21_16100, APD31_02670, AUO97_04875, AYR68_16515, B7L36_04505, B7L45_01975, B9X95_19475, BAA1790NC_0315, BS065_01600, C2U32_12605, C5H40_03430, C6N18_18350, CBE85_06420, CBL15_01550, CSB70_3370, CTZ19_01585, DLI71_12465, DLI72_03665, DOL94_17785, E1A86_17370, E2535_18555, E2539_03475, E2540_19450, EA686_01605, EA706_01570, EA720_012255, EA722_01135, EGM95_01775, EKS29_00960, EP550_01655, EP560_16360, EWO96_11255, F2P40_01005, F4T85_13595, F4T91_15305, FDN00_18830, FE003_01590, FJU36_10385, FJU42_02940, FJU59_00430, FJU76_08505, FR761_17725, GNY86_13750, GSE42_18470, H0529_17955, H1058_16860, HBK86_16410, HIN86_01600, IMO23_16495, NCTC13305_02770, NCTC13421_00317, SAMEA104305281_00293, SAMEA104305340_01315, SAMEA104305385_01516, SI89_16095 EC: 2.7.6.5 (PDB Primary Data), 3.1.7.2 (UniProt)
UniProt
Find proteins for V5V8V7 (Acinetobacter baumannii) Explore V5V8V7 Go to UniProtKB: V5V8V7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	V5V8V7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4P (Subject of Investigation/LOI) Query on G4P Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain Y [auth D]	G [auth A], M [auth B], Q [auth C], Y [auth D]	GUANOSINE-5',3'-TETRAPHOSPHATE C₁₀ H₁₇ N₅ O₁₇ P₄ BUFLLCUFNHESEH-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain Y [auth D]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain R [auth C]	H [auth A], R [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain R [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	I [auth A], N [auth B], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain X [auth D]	F [auth A], L [auth B], P [auth C], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain X [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain W [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain W [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain W [auth D]	E [auth A], K [auth B], O [auth C], W [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain V [auth C]	AA [auth D], J [auth A], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain V [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	U [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain U [auth C] Focus chain Z [auth D]