5BK2

Crystal structure of maltose binding protein in complex with a peristeric synthetic antibody

• PDB DOI: https://doi.org/10.2210/pdb5BK2/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-09-12 Released: 2018-01-17 
• Deposition Author(s): Mukherjee, S., Kossiakoff, A.A.
• Funding Organization(s): Chicago Biomedical Consortium

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 188.84 kDa 
• Atom Count: 12,849 
• Modelled Residue Count: 1,614 
• Deposited Residue Count: 1,702 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	A [auth B], B [auth A]	398	Escherichia coli K-12	Mutation(s): 0  Gene Names: malE, b4034, JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
sAB Heavy Chain	C, D [auth H]	237	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
sAB Light Chain	E [auth D], F [auth L]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	AA [auth H], CA [auth D], S [auth C], Z [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	DA [auth L], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C], T [auth H], U [auth H], V [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	BA [auth D], I [auth B], J [auth A], R [auth C], W [auth H], X [auth H], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	G [auth E], H [auth F]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.259 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.17	α = 90
b = 42.38	β = 90.07
c = 200.66	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MD2	data collection
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Mukherjee, S., Kossiakoff, A.A.

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Funding Organization	Location	Grant Number
Chicago Biomedical Consortium	United States	--

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary