3ZYB | pdb_00003zyb

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALAG0 AT 2.3 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3ZYB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-19 Released: 2011-09-21
Deposition Author(s): Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.240 (Depositor), 0.236 (DCC)
R-Value Work:
0.214 (Depositor), 0.208 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

A Glycopeptide Dendrimer Inhibitor of the Galactose-Specific Lectin Leca and of Pseudomonas Aeruginosa Biofilms.

Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

(2011) Angew Chem Int Ed Engl 50: 10631

PubMed: 21919164 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.201104342
Primary Citation Related Structures:
3ZYB, 3ZYF, 3ZYH

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.

Macromolecule Content

Total Structure Weight: 107.14 kDa
Atom Count: 8,394
Modeled Residue Count: 980
Deposited Residue Count: 988
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I galactophilic lectin	A, B, C, D, E A, B, C, D, E, F, G, H	122	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lecA, pa1L, PA2570
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097 Go to UniProtKB: Q05097
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GALA-LYS-PRO-LEUNH2	I, J, K [auth N]	4	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain P [auth B] SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain M [auth A] SDF format, chain HA [auth H] SDF format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain BA [auth F]	BA [auth F] EA [auth G] HA [auth H] M [auth A] P [auth B] BA [auth F], EA [auth G], HA [auth H], M [auth A], P [auth B], S [auth C], V [auth D], Y [auth E]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
PHB Query on PHB Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain IA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] IA [auth H] N [auth A] Q [auth B] CA [auth F], FA [auth G], IA [auth H], N [auth A], Q [auth B], T [auth C], W [auth D], Z [auth E]	P-HYDROXYBENZOIC ACID C₇ H₆ O₃ FJKROLUGYXJWQN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain GA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] GA [auth H] L [auth A] O [auth B] AA [auth F], DA [auth G], GA [auth H], L [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	BindingDB: 3ZYB	Kd: 8.75e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.240 (Depositor), 0.236 (DCC)
R-Value Work: 0.214 (Depositor), 0.208 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.332	α = 90
b = 128.559	β = 90
c = 146.063	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2012-04-25
Changes: Other
Version 1.2: 2017-02-08
Changes: Source and taxonomy
Version 1.3: 2017-07-12
Changes: Derived calculations
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-11-06
Changes: Structure summary