6EQ0

Structure of the periplasmic binding protein (PBP) MelB (atu4661) in complex with galactose from agrobacterium tumefacien C58

PDB DOI: https://doi.org/10.2210/pdb6EQ0/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Agrobacterium tumefaciens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-10-12 Released: 2018-04-11
Deposition Author(s): Vigouroux, A., Morera, S.
Funding Organization(s): CNRS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.241
R-Value Work: 0.194
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 155.84 kDa
Atom Count: 10,998
Modelled Residue Count: 1,342
Deposited Residue Count: 1,366
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic alpha-galactoside-binding protein	A, B	683	Agrobacterium tumefaciens	Mutation(s): 0 Gene Names: SY94_4618
UniProt
Find proteins for A0A083ZM57 (Rhizobium radiobacter) Explore A0A083ZM57 Go to UniProtKB: A0A083ZM57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A083ZM57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain C [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain C [auth A]	C [auth A], LA [auth B]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain C [auth A] Focus chain LA [auth B] Interactions & Density Focus chain C [auth A] Focus chain LA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain SA [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain RA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DB [auth B] SDF format, chain EB [auth B] SDF format, chain FB [auth B] SDF format, chain JA [auth A] SDF format, chain Z [auth A] SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain IA [auth A] SDF format, chain KA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain KA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] DB [auth B] AA [auth A], BA [auth A], CA [auth A], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], JA [auth A], KA [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain Z [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain AB [auth B] SDF format, chain CB [auth B] SDF format, chain Q [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain ZA [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain AB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain ZA [auth B]	AB [auth B] BB [auth B] CB [auth B] Q [auth A] R [auth A] AB [auth B], BB [auth B], CB [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], ZA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZA [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
GLA	Binding MOAD: 6EQ0	Kd: 2.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.241
R-Value Work: 0.194
R-Value Observed: 0.196
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.84	α = 90
b = 73.92	β = 92.55
c = 171.1	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-04-11

Deposition Author(s):

Vigouroux, A.

Morera, S.

Funding Organization	Location	Grant Number
CNRS	France	MI

Revision History (Full details and data files)

Version 1.0: 2018-04-11
Type: Initial release
Version 1.1: 2018-06-06
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary