1LRH

Crystal structure of auxin-binding protein 1 in complex with 1-naphthalene acetic acid

PDB DOI: https://doi.org/10.2210/pdb1LRH/pdb

Classification: PROTEIN BINDING
Organism(s): Zea mays
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2002-05-15 Released: 2002-06-19
Deposition Author(s): Woo, E.J., Marshall, J., Bauly, J., Chen, J.-G., Venis, M., Napier, R.M., Pickersgill, R.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of auxin-binding protein 1 in complex with auxin.

Woo, E.J., Marshall, J., Bauly, J., Chen, J.G., Venis, M., Napier, R.M., Pickersgill, R.W.

(2002) EMBO J 21: 2877-2885

PubMed: 12065401 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/emboj/cdf291
Primary Citation of Related Structures:
1LR5, 1LRH

PubMed Abstract:
The structure of auxin-binding protein 1 (ABP1) from maize has been determined at 1.9 A resolution, revealing its auxin-binding site. The structure confirms that ABP1 belongs to the ancient and functionally diverse germin/seed storage 7S protein superfamily. The binding pocket of ABP1 is predominantly hydrophobic with a metal ion deep inside the pocket coordinated by three histidines and a glutamate. Auxin binds within this pocket, with its carboxylate binding the zinc and its aromatic ring binding hydrophobic residues including Trp151. There is a single disulfide between Cys2 and Cys155. No conformational rearrangement of ABP1 was observed when auxin bound to the protein in the crystal, but examination of the structure reveals a possible mechanism of signal transduction.

Organizational Affiliation

Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK.

Macromolecule Content

Total Structure Weight: 78.95 kDa
Atom Count: 5,799
Modelled Residue Count: 640
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
auxin-binding protein 1	A, B, C, D	163	Zea mays	Mutation(s): 2 Gene Names: ABP1
UniProt
Find proteins for P13689 (Zea mays) Explore P13689 Go to UniProtKB: P13689
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13689
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	6		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NLA Query on NLA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D]	J [auth A], L [auth B], N [auth C], P [auth D]	NAPHTHALEN-1-YL-ACETIC ACID C₁₂ H₁₀ O₂ PRPINYUDVPFIRX-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	I [auth A], K [auth B], M [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
NLA	PDBBind: 1LRH	Kd: 150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.583	α = 90
b = 82.433	β = 94.37
c = 69.962	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-06-19
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-11-10
Changes: Database references, Structure summary
Version 2.2: 2024-11-13
Changes: Data collection, Structure summary