9DL8

Structure of proline utilization A soaked with 4-methoxybenzyl alcohol

PDB DOI: https://doi.org/10.2210/pdb9DL8/pdb

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

Deposited: 2024-09-10 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: 1.64 Å
R-Value Free: 0.193
R-Value Work: 0.166
R-Value Observed: 0.167

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: 271.54 kDa
Atom Count: 20,125
Modelled Residue Count: 2,407
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 CA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain CA [auth B]	C [auth A], CA [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain CA [auth B] Interactions & Density Focus chain C [auth A] Focus chain CA [auth B]
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain UA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain UA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain UA [auth B]	UA [auth B], X [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain UA [auth B] Focus chain X [auth A] Interactions & Density Focus chain UA [auth B] Focus chain X [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain T [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain T [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain T [auth A]	LA [auth B], NA [auth B], O [auth A], T [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain T [auth A] Interactions & Density Focus chain LA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Focus chain T [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth A] SDF format, chain PA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth B]	EA [auth B], M [auth A], PA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain M [auth A] Focus chain PA [auth B] Interactions & Density Focus chain EA [auth B] Focus chain M [auth A] Focus chain PA [auth B]
A1BDD (Subject of Investigation/LOI) Query on A1BDD Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A]	JA [auth B], K [auth A]	(4-methoxyphenyl)methanol C₈ H₁₀ O₂ MSHFRERJPWKJFX-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain K [auth A] Interactions & Density Focus chain JA [auth B] Focus chain K [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain TA [auth B] SDF format, chain V [auth A] SDF format, chain DA [auth B] SDF format, chain GA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain MA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth B]	D [auth A] DA [auth B] E [auth A] F [auth A] FA [auth B] D [auth A], DA [auth B], E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], KA [auth B], L [auth A], MA [auth B], N [auth A], Q [auth A], R [auth A], RA [auth B], S [auth A], TA [auth B], V [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain TA [auth B] Focus chain V [auth A] Interactions & Density Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain TA [auth B] Focus chain V [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] VA [auth B] WA [auth B] Y [auth A] AA [auth A], BA [auth A], VA [auth B], WA [auth B], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain QA [auth B] SDF format, chain SA [auth B] SDF format, chain U [auth A] SDF format, chain W [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A]	OA [auth B] P [auth A] QA [auth B] SA [auth B] U [auth A] OA [auth B], P [auth A], QA [auth B], SA [auth B], U [auth A], W [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain OA [auth B] Focus chain P [auth A] Focus chain QA [auth B] Focus chain SA [auth B] Focus chain U [auth A] Focus chain W [auth A] Interactions & Density Focus chain OA [auth B] Focus chain P [auth A] Focus chain QA [auth B] Focus chain SA [auth B] Focus chain U [auth A] Focus chain W [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain XA [auth B] MOL2 format, chain XA [auth B] mmCIF format, chain XA [auth B]	XA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain XA [auth B] Interactions & Density Focus chain XA [auth B]