3WMP

Crystal structure of SLL-2

PDB DOI: https://doi.org/10.2210/pdb3WMP/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Sinularia lochmodes
Mutation(s): No

Deposited: 2013-11-22 Released: 2015-01-14
Deposition Author(s): Kita, A., Jimbo, M., Sakai, R., Morimoto, Y., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.271
R-Value Work: 0.251
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 68.64 kDa
Atom Count: 4,887
Modelled Residue Count: 564
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose-binding lectin	A, B, C, D, E A, B, C, D, E, F	94	Sinularia lochmodes	Mutation(s): 0
UniProt
Find proteins for A4CYJ6 (Sinularia lochmodes) Explore A4CYJ6 Go to UniProtKB: A4CYJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4CYJ6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C]	T [auth C]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
GLA Query on GLA Download Ideal Coordinates CCD File SDF format, chain FA [auth F] MOL2 format, chain FA [auth F]	FA [auth F]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain FA [auth F] Interactions & Density Focus chain FA [auth F]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain U [auth C] SDF format, chain Y [auth D] MOL2 format, chain M [auth A] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth D]	M [auth A], U [auth C], Y [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain M [auth A] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain M [auth A] Focus chain U [auth C] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D]	AA [auth D] CA [auth E] DA [auth E] GA [auth F] HA [auth F] AA [auth D], CA [auth E], DA [auth E], GA [auth F], HA [auth F], N [auth A], O [auth A], Q [auth B], R [auth B], V [auth C], W [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain IA [auth F] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain IA [auth F] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C]	BA [auth D] EA [auth E] IA [auth F] P [auth A] S [auth B] BA [auth D], EA [auth E], IA [auth F], P [auth A], S [auth B], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain P [auth A] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain IA [auth F] Focus chain P [auth A] Focus chain S [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.271
R-Value Work: 0.251
R-Value Observed: 0.251
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.03	α = 90
b = 189.95	β = 110.55
c = 57.05	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-09-23
Changes: Database references, Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary