4MQ0 | pdb_00004mq0

Crystal structure of Parkia biglobosa seed lectin (PBL) in complex with methyl alpha D-mannopyranoside

• PDB DOI: https://doi.org/10.2210/pdb4MQ0/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Parkia biglobosa
• Mutation(s): No 


• Deposited: 2013-09-14 Released: 2014-12-17 
• Deposition Author(s): Teixeira, C.S., Rocha, B.A.M., Silva, H.C., Bari, A.U., Barroso-Neto, I.L., Santiago, M.Q., Nagano, C.S., Nascimento, K.S., Debray, H., Delatorre, P., Cavada, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.293 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Crystal structure of Parkia biglobosa seed lectin (PBL) in complex with methyl alpha D-mannopyranoside

Teixeira, C.S., Rocha, B.A.M., Silva, H.C., Bari, A.U., Barroso-Neto, I.T., Santiago, M.Q., Nagano, C.S., Nascimento, K.S., Debray, H., Delatorre, P., Cavada, B.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 48.2 kDa 
• Atom Count: 3,440 
• Modeled Residue Count: 438 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parkia biglobosa lectin (PBL)	A	446	Parkia biglobosa	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMA	B [auth A], C [auth A], D [auth A]	methyl alpha-D-mannopyranoside C7 H14 O6 HOVAGTYPODGVJG-VEIUFWFVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.293 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.139	α = 90
b = 86.659	β = 90
c = 127.857	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Teixeira, C.S., Rocha, B.A.M., Silva, H.C., Bari, A.U., Barroso-Neto, I.L., Santiago, M.Q., Nagano, C.S., Nascimento, K.S., Debray, H., Delatorre, P., Cavada, B.S.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Structure summary