8CG1 | pdb_00008cg1

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H12

PDB DOI: https://doi.org/10.2210/pdb8CG1/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-02-03 Released: 2024-02-21
Deposition Author(s): Malecki, P.H., Gawel, M., Stepniewska, M., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

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

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry H12

Malecki, P.H., Gawel, M., Stepniewska, M., Brzezinski, K.

To be published.

Macromolecule Content

Total Structure Weight: 423.67 kDa
Atom Count: 31,781
Modeled Residue Count: 3,692
Deposited Residue Count: 3,776
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A B C D E [auth G] A, B, C, D, E [auth G], F [auth H], G [auth I], H [auth J]	472	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ahcY, sahH, PA0432 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I685 Go to UniProtKB: Q9I685
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain GB [auth J] SDF format, chain I [auth A] SDF format, chain JA [auth G] SDF format, chain P [auth B] SDF format, chain QA [auth H] SDF format, chain V [auth C] SDF format, chain YA [auth I] MOL2 format, chain CA [auth D] MOL2 format, chain GB [auth J] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain YA [auth I] mmCIF format, chain CA [auth D] mmCIF format, chain GB [auth J] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain YA [auth I]	CA [auth D] GB [auth J] I [auth A] JA [auth G] P [auth B] CA [auth D], GB [auth J], I [auth A], JA [auth G], P [auth B], QA [auth H], V [auth C], YA [auth I]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth D] Focus chain GB [auth J] Focus chain I [auth A] Focus chain JA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain V [auth C] Focus chain YA [auth I] Interactions & Density Focus chain CA [auth D] Focus chain GB [auth J] Focus chain I [auth A] Focus chain JA [auth G] Focus chain P [auth B] Focus chain QA [auth H] Focus chain V [auth C] Focus chain YA [auth I]
SZA (Subject of Investigation/LOI) Query on SZA Download Ideal Coordinates CCD File SDF format, chain SA [auth H] MOL2 format, chain SA [auth H] mmCIF format, chain SA [auth H]	SA [auth H]	~{N}-(2-thiophen-2-ylethyl)pyridine-4-carboxamide C₁₂ H₁₂ N₂ O S MBRRKSONRBUYSE-UHFFFAOYSA-N		Interactions Focus chain SA [auth H] Interactions & Density Focus chain SA [auth H]
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain HB [auth J] SDF format, chain J [auth A] SDF format, chain KA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain W [auth C] SDF format, chain ZA [auth I] MOL2 format, chain DA [auth D] MOL2 format, chain HB [auth J] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain ZA [auth I] mmCIF format, chain DA [auth D] mmCIF format, chain HB [auth J] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain ZA [auth I]	DA [auth D] HB [auth J] J [auth A] KA [auth G] Q [auth B] DA [auth D], HB [auth J], J [auth A], KA [auth G], Q [auth B], RA [auth H], W [auth C], ZA [auth I]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain HB [auth J] Focus chain J [auth A] Focus chain KA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain W [auth C] Focus chain ZA [auth I] Interactions & Density Focus chain DA [auth D] Focus chain HB [auth J] Focus chain J [auth A] Focus chain KA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain W [auth C] Focus chain ZA [auth I]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CB [auth I] SDF format, chain DB [auth I] SDF format, chain EB [auth I] SDF format, chain FB [auth I] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JB [auth J] SDF format, chain KB [auth J] SDF format, chain L [auth A] SDF format, chain LB [auth J] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain VA [auth H] SDF format, chain WA [auth H] SDF format, chain XA [auth H] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth I] MOL2 format, chain DB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain FB [auth I] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JB [auth J] MOL2 format, chain KB [auth J] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth J] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth H] MOL2 format, chain XA [auth H] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth I] mmCIF format, chain DB [auth I] mmCIF format, chain EB [auth I] mmCIF format, chain FB [auth I] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JB [auth J] mmCIF format, chain KB [auth J] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth J] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain WA [auth H] mmCIF format, chain XA [auth H] mmCIF format, chain Z [auth C]	AA [auth C] BA [auth C] CB [auth I] DB [auth I] EB [auth I] AA [auth C], BA [auth C], CB [auth I], DB [auth I], EB [auth I], FB [auth I], GA [auth D], HA [auth D], IA [auth D], JB [auth J], KB [auth J], L [auth A], LB [auth J], M [auth A], MA [auth G], N [auth A], NA [auth G], O [auth A], OA [auth G], PA [auth G], T [auth B], U [auth B], VA [auth H], WA [auth H], XA [auth H], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain FB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain L [auth A] Focus chain LB [auth J] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain FB [auth I] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JB [auth J] Focus chain KB [auth J] Focus chain L [auth A] Focus chain LB [auth J] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain T [auth B] Focus chain U [auth B] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Z [auth C]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain EA [auth D] SDF format, chain R [auth B] SDF format, chain TA [auth H] SDF format, chain X [auth C] MOL2 format, chain AB [auth I] MOL2 format, chain EA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain X [auth C] mmCIF format, chain AB [auth I] mmCIF format, chain EA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain X [auth C]	AB [auth I], EA [auth D], R [auth B], TA [auth H], X [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain EA [auth D] Focus chain R [auth B] Focus chain TA [auth H] Focus chain X [auth C] Interactions & Density Focus chain AB [auth I] Focus chain EA [auth D] Focus chain R [auth B] Focus chain TA [auth H] Focus chain X [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BB [auth I] SDF format, chain FA [auth D] SDF format, chain IB [auth J] SDF format, chain K [auth A] SDF format, chain LA [auth G] SDF format, chain S [auth B] SDF format, chain UA [auth H] SDF format, chain Y [auth C] MOL2 format, chain BB [auth I] MOL2 format, chain FA [auth D] MOL2 format, chain IB [auth J] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain Y [auth C] mmCIF format, chain BB [auth I] mmCIF format, chain FA [auth D] mmCIF format, chain IB [auth J] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain Y [auth C]	BB [auth I] FA [auth D] IB [auth J] K [auth A] LA [auth G] BB [auth I], FA [auth D], IB [auth J], K [auth A], LA [auth G], S [auth B], UA [auth H], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BB [auth I] Focus chain FA [auth D] Focus chain IB [auth J] Focus chain K [auth A] Focus chain LA [auth G] Focus chain S [auth B] Focus chain UA [auth H] Focus chain Y [auth C] Interactions & Density Focus chain BB [auth I] Focus chain FA [auth D] Focus chain IB [auth J] Focus chain K [auth A] Focus chain LA [auth G] Focus chain S [auth B] Focus chain UA [auth H] Focus chain Y [auth C]