7W62 | pdb_00007w62

Mevo lectin complex with mannotetraose (Man4)

• PDB DOI: https://doi.org/10.2210/pdb7W62/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Methanococcus voltae A3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-01 Released: 2023-01-18 
• Deposition Author(s): Sivaji, N., Vijayan, M.
• Funding Organization(s): Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Mevo lectin complex with mannotetraose (Man4)

Sivaji, N., Vijayan, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Homo 7-mer - A7 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 230.42 kDa 
• Atom Count: 16,060 
• Modeled Residue Count: 1,962 
• Deposited Residue Count: 2,030 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lectin	A [auth B], B [auth G], C [auth A], D, E, F, G [auth C], H, I, J, K, L, M, N	145	Methanococcus voltae A3	Mutation(s): 0  Gene Names: Mvol_0737
UniProt
Find proteins for D7DTD6 (Methanococcus voltae (strain ATCC BAA-1334 / A3)) Explore D7DTD6  Go to UniProtKB:  D7DTD6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	AA [auth a], BA [auth b], O, P, Q, S, U, V, W, X, Y, Z	4		N/A
Glycosylation Resources
GlyTouCan:  G77865AH GlyCosmos:  G77865AH GlyGen:  G77865AH

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	R, T	3		N/A
Glycosylation Resources
GlyTouCan:  G25559RS GlyCosmos:  G25559RS GlyGen:  G25559RS

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	CA [auth D], DA [auth F], EA [auth C], FA [auth H], GA [auth K], HA [auth K], IA [auth M]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.21	α = 90
b = 168.3	β = 90
c = 170.249	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Sivaji, N., Vijayan, M.

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Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	--

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description