8JV2 | pdb_00008jv2

Structure of the SAR11 PotD in complex with proline

PDB DOI: https://doi.org/10.2210/pdb8JV2/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Candidatus Pelagibacter sp. HTCC7211
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-27 Released: 2024-07-03
Deposition Author(s): Ma, Q., Liu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.134 (Depositor), 0.146 (DCC)
R-Value Work:
0.119 (Depositor), 0.135 (DCC)
R-Value Observed:
0.120 (Depositor)

Starting Model: in silico
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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 the SAR11 PotD in complex with proline

Ma, Q., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 40.33 kDa
Atom Count: 3,281
Modeled Residue Count: 360
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine/putrescine-binding periplasmic protein	A	361	Candidatus Pelagibacter sp. HTCC7211	Mutation(s): 0 Gene Names: potD, PB7211_697
UniProt
Find proteins for A0ACD6B9P1 (Pelagibacter sp. (strain HTCC7211)) Explore A0ACD6B9P1 Go to UniProtKB: A0ACD6B9P1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9P1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PRO (Subject of Investigation/LOI) Query on PRO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]