3PUZ

Crystal Structure of a pre-translocation state MBP-Maltose transporter complex bound to AMP-PNP

PDB DOI: https://doi.org/10.2210/pdb3PUZ/pdb

Classification: TRANSPORT PROTEIN, MEMBRANE PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2010-12-06 Released: 2011-05-18
Deposition Author(s): Oldham, M.L., Chen, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.279
R-Value Work: 0.237
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 216.98 kDa
Atom Count: 14,697
Modelled Residue Count: 1,873
Deposited Residue Count: 1,942
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transporter subunit; periplasmic-binding component of ABC superfamily	A [auth E]	370	Escherichia coli K-12	Mutation(s): 2 Gene Names: ECDH10B_4223, malE Membrane Entity: Yes
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AEX9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transporter subunit; membrane component of ABC superfamily	B [auth F]	514	Escherichia coli K-12	Mutation(s): 0 Gene Names: ECDH10B_4222, malF Membrane Entity: Yes
UniProt
Find proteins for P02916 (Escherichia coli (strain K12)) Explore P02916 Go to UniProtKB: P02916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02916
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose transporter subunit; membrane component of ABC superfamily	C [auth G]	296	Escherichia coli K-12	Mutation(s): 0 Gene Names: ECDH10B_4221, malG Membrane Entity: Yes
UniProt
Find proteins for P68183 (Escherichia coli (strain K12)) Explore P68183 Go to UniProtKB: P68183
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68183
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fused maltose transport subunit, ATP-binding component of ABC superfamily; regulatory protein	D [auth A], E [auth B]	381	Escherichia coli K-12	Mutation(s): 0 Gene Names: ECDH10B_4224, malK Membrane Entity: Yes
UniProt
Find proteins for P68187 (Escherichia coli (strain K12)) Explore P68187 Go to UniProtKB: P68187
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68187
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F [auth C], G [auth D]	2		N/A	Interactions Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain F [auth C] Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGV Query on PGV Download Ideal Coordinates CCD File SDF format, chain H [auth F] MOL2 format, chain H [auth F]	H [auth F]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B]	J [auth A], L [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B]	I [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain K [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	F [auth C], G [auth D]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain F [auth C] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.279
R-Value Work: 0.237
R-Value Observed: 0.239
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.021	α = 90.05
b = 93.36	β = 102.57
c = 119.761	γ = 105.01

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-05-18

Deposition Author(s):

Oldham, M.L.

Chen, J.

Revision History (Full details and data files)

Version 1.0: 2011-05-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary