9J1C | pdb_00009j1c

Structure of ConA/NAP-Man

PDB DOI: https://doi.org/10.2210/pdb9J1C/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: 2.43 Å
R-Value Free:
0.282 (Depositor), 0.278 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.215 (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/NAP-Man

Li, L., Chen, G.

To be published.

Macromolecule Content

Total Structure Weight: 104.3 kDa
Atom Count: 7,344
Modeled Residue Count: 948
Deposited Residue Count: 948
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, C, D	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
A1EAU (Subject of Investigation/LOI) Query on A1EAU Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	G [auth B], J [auth C]	~{N}2,~{N}6-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]naphthalene-2,6-dicarboxamide C₃₂ H₄₆ N₂ O₁₆ IGDPOUCLGLHGCQ-IEOQPZBNSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	F [auth A], I [auth B], L [auth C], N [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]