9UP2 | pdb_00009up2

PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)

PDB DOI: https://doi.org/10.2210/pdb9UP2/pdb
EM Map EMD-64387: EMDB EMDataResource

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

Deposited: 2025-04-27 Released: 2026-04-01
Deposition Author(s): Cao, W., Wang, J., Wang, Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UP2

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

Literature

Analysis of heterocycle formation and stereochemical control by a non-ribosomal peptide synthetase condensation domain

Cao, W., Wang, J., Chen, S.L., Li, D., Wang, X., Deng, Z., Liang, J., Wang, Z.

(2026) Nat Synth

DOI: https://doi.org/10.1038/s44160-026-01014-7

Macromolecule Content

Total Structure Weight: 180.56 kDa
Atom Count: 12,720
Modeled Residue Count: 1,597
Deposited Residue Count: 1,597
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PvdL	A	1,536	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: pvdL, PA2424
UniProt
Find proteins for Q9I157 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I157 Go to UniProtKB: Q9I157
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I157
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MbtH-like domain-containing protein	B	61	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA2412
UniProt
Find proteins for Q9I169 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I169 Go to UniProtKB: Q9I169
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I169
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
DAB Query on DAB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A]	C [auth A], E [auth A]	2,4-DIAMINOBUTYRIC ACID C₄ H₁₀ N₂ O₂ OGNSCSPNOLGXSM-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4HH Query on 4HH	A	L-PEPTIDE LINKING	C₁₄ H₂₈ N₃ O₉ P S		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.33 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	2021YFA0910500

Revision History (Full details and data files)

Version 1.0: 2026-04-01
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.