9E0B

Structure of proline utilization A complexed with (2,3-dihydro-1-benzofuran-5-yl)methanol

PDB DOI: https://doi.org/10.2210/pdb9E0B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti SM11
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-17 Released: 2024-11-27
Deposition Author(s): Tanner, J.J., Meeks, K.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.200
R-Value Work: 0.177
R-Value Observed: 0.178

Starting Model: experimental
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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

Crystallographic Fragment Screening of a Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates for Proline Dehydrogenase and L-Glutamate-gamma-semialdehyde Dehydrogenase

Meeks, K.R., Bogner, A.N., Nix, J.C., Tanner, J.J.

(2024) Molecules 29

DOI: https://doi.org/10.3390/molecules29225408

Macromolecule Content

Total Structure Weight: 269.05 kDa
Atom Count: 20,493
Modelled Residue Count: 2,423
Deposited Residue Count: 2,470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein PutA	A, B	1,235	Sinorhizobium meliloti SM11	Mutation(s): 0 Gene Names: putA, SM11_chr0102 EC: 1.5.5.2 (PDB Primary Data), 1.2.1.88 (PDB Primary Data)
UniProt
Find proteins for F7X6I3 (Sinorhizobium meliloti (strain SM11)) Explore F7X6I3 Go to UniProtKB: F7X6I3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F7X6I3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain I [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain I [auth A]	AA [auth B], I [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth B] Focus chain I [auth A] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
A1AQC (Subject of Investigation/LOI) Query on A1AQC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Y [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Y [auth B]	F [auth A], Y [auth B]	(2,3-dihydro-1-benzofuran-5-yl)methanol C₉ H₁₀ O₂ XQDNBMXUZGAWSZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain Y [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth B]	D [auth A] DA [auth B] T [auth B] U [auth B] V [auth B] D [auth A], DA [auth B], T [auth B], U [auth B], V [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain DA [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain DA [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	BA [auth B] J [auth A] K [auth A] L [auth A] M [auth A] BA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain BA [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	E [auth A] G [auth A] H [auth A] S [auth B] W [auth B] E [auth A], G [auth A], H [auth A], S [auth B], W [auth B], X [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain W [auth B] Focus chain X [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain O [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain O [auth A]	CA [auth B], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain O [auth A] Interactions & Density Focus chain CA [auth B] Focus chain O [auth A]