9J1B | pdb_00009j1b

Structure of ConA/IMI-Man

PDB DOI: https://doi.org/10.2210/pdb9J1B/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Canavalia ensiformis
Mutation(s): No

Deposited: 2024-08-04 Released: 2024-12-04
Deposition Author(s): Li, L., Chen, G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.228 (Depositor), 0.231 (DCC)
R-Value Work:
0.188 (Depositor), 0.193 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of ConA/IMI-Man

Li, L., Chen, G.

To be published.

Macromolecule Content

Total Structure Weight: 52.15 kDa
Atom Count: 3,688
Modeled Residue Count: 474
Deposited Residue Count: 474
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin-A	A, B	237	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P02866 (Canavalia ensiformis) Explore P02866 Go to UniProtKB: P02866
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02866
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EAT (Subject of Investigation/LOI) Query on A1EAT Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	~{N}-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethyl]-4-[3-[4-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethylcarbamoyl]phenyl]imidazol-3-ium-1-yl]benzamide C₃₃ H₄₃ N₄ O₁₄ YIHGTVGPQNMBCK-QIXJGXQISA-O		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]