8HYF | pdb_00008hyf

Crystal Structure of Banana Lectin In-complex with Fucose at 2.95 A Resolution

PDB DOI: https://doi.org/10.2210/pdb8HYF/pdb

Classification: SUGAR BINDING PROTEIN, ANTITUMOR PROTEIN
Organism(s): Musa x paradisiaca
Mutation(s): No

Deposited: 2023-01-06 Released: 2024-01-17
Deposition Author(s): Rasheed, S., Arif, R., Huda, N., Ahmad, M.S., Mateen, S.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.253 (Depositor), 0.253 (DCC)
R-Value Work:
0.192 (Depositor), 0.192 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

Crystal Structure of Banana Lectin in-Complex with L-Fucose at 2.95 A Resolution

Rasheed, S., Arif, R., Huda, N., Ahmad, M.S., Mateen, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 30.53 kDa
Atom Count: 2,202
Modeled Residue Count: 280
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ripening-associated protein	A, B	141	Musa x paradisiaca	Mutation(s): 0
UniProt
Find proteins for O22321 (Musa acuminata) Explore O22321 Go to UniProtKB: O22321
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O22321
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC (Subject of Investigation/LOI) Query on FUC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] J [auth B] K [auth B] L [auth B] C [auth A], D [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.253 (Depositor), 0.253 (DCC)
R-Value Work: 0.192 (Depositor), 0.192 (DCC)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.219	α = 90
b = 81.219	β = 90
c = 147.315	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PROTEUM	data collection
Aimless	data scaling
MOLREP	phasing
PROTEUM PLUS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		Not funded

Revision History (Full details and data files)

Version 1.0: 2024-01-17
Type: Initial release
Version 2.0: 2024-12-11
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.0: 2025-10-22
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary