9E2B | pdb_00009e2b

Structure of a solute binding protein from Desulfonauticus sp. bound to L-tryptophan

PDB DOI: https://doi.org/10.2210/pdb9E2B/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Desulfonauticus sp. 38_4375
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-22 Released: 2024-11-06
Deposition Author(s): Rahman, M., Frkic, R.L., Smith, O.B., Jackson, C.J.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.185 (Depositor), 0.184 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of a solute binding protein from Desulfonauticus sp. bound to L-tryptophan

Rahman, M., Frkic, R.L., Smith, O.B., Jackson, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 187.2 kDa
Atom Count: 13,301
Modeled Residue Count: 1,517
Deposited Residue Count: 1,620
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type transporter, periplasmic subunit family 3	A, B, C, D, E A, B, C, D, E, F	270	Desulfonauticus sp. 38_4375	Mutation(s): 0 Gene Names: XD41_0486
UniProt
Find proteins for A0ACD6B9Y2 (Desulfonauticus sp. 38_4375) Explore A0ACD6B9Y2 Go to UniProtKB: A0ACD6B9Y2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRP (Subject of Investigation/LOI) Query on TRP Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain KA [auth F] SDF format, chain G [auth A] SDF format, chain EA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain EA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain EA [auth E]	EA [auth E] G [auth A] KA [auth F] O [auth B] R [auth C] EA [auth E], G [auth A], KA [auth F], O [auth B], R [auth C], X [auth D]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain EA [auth E] Focus chain G [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain R [auth C] Focus chain X [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] MOL2 format, chain FA [auth E] mmCIF format, chain FA [auth E]	FA [auth E]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Interactions & Density Focus chain FA [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain S [auth C] SDF format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B]	Q [auth B], S [auth C], Y [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain Q [auth B] Focus chain S [auth C] Focus chain Y [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain OA [auth F] SDF format, chain NA [auth F] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth E] SDF format, chain I [auth A] SDF format, chain HA [auth E] SDF format, chain H [auth A] SDF format, chain GA [auth E] SDF format, chain DA [auth D] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] DA [auth D] GA [auth E] H [auth A] AA [auth D], BA [auth D], DA [auth D], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], JA [auth E], K [auth A], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], NA [auth F], OA [auth F], P [auth B], T [auth C], U [auth C], W [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain DA [auth D] Focus chain GA [auth E] Focus chain H [auth A] Focus chain HA [auth E] Focus chain I [auth A] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain Z [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain CA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain CA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain CA [auth D]	CA [auth D], V [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CA [auth D] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain V [auth C]