Structure of PDB 3c5m Chain B Binding Site BS01

Receptor Information

>3c5m Chain B (length=378) Species: 223926 (Vibrio parahaemolyticus RIMD 2210633) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AKGDVITLNFETFVDSDTQVKVTRLTPTDIICHRNYFYQKCFTQDGKKLL
FAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNE
LNLMKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQP
LTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDS
TVGFCHEGPHDLVDARMWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSA
MAYVSYFKGQTDRVIYKANPETLENEEVMVMPPCSHLMSNFDGSLMVGDG
CDAPVNIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFT
PNDDGVLFTSDFEGVPAIYIADVPESYK

Ligand information

Ligand ID

InChI

InChI=1S/Mn/q+2

InChIKey

WAEMQWOKJMHJLA-UHFFFAOYSA-N

SMILES

Software	SMILES
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Mn+2]
CACTVS 3.341	[Mn++]

Formula

Name

MANGANESE (II) ION

PDB chain

3c5m Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	3c5m Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus.
Resolution	2.6 Å
Binding residue (original residue number in PDB)	H287 Q350 H353 H355
Binding residue (residue number reindexed from 1)	H286 Q341 H344 H346
Annotation score	1

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0016829	lyase activity
GO:0046872	metal ion binding
GO:0047487	oligogalacturonide lyase activity

	Biological Process
GO:0045490	pectin catabolic process

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:3c5m, PDBe:3c5m, PDBj:3c5m
PDBsum	3c5m
PubMed
UniProt	Q87K10

[Back to BioLiP]