6T9B

Crystal structrue of RSL W31A lectin mutant in complex with alpha-methylfucoside

PDB DOI: https://doi.org/10.2210/pdb6T9B/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ralstonia solanacearum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-10-26 Released: 2020-04-22
Deposition Author(s): Houser, J., Komarek, J., Kozmon, S., Wimmerova, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.211
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 90.37 kDa
Atom Count: 7,479
Modelled Residue Count: 788
Deposited Residue Count: 810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin protein	A, B, C, D, E A, B, C, D, E, F, G, H, I	90	Ralstonia solanacearum	Mutation(s): 1 Gene Names: RSP795_21825, RSP799_05830, RSP822_19650, RUN39_v1_50103
UniProt
Find proteins for A0A0S4TLR1 (Ralstonia solanacearum) Explore A0A0S4TLR1 Go to UniProtKB: A0A0S4TLR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0S4TLR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MFU (Subject of Investigation/LOI) Query on MFU Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain BA [auth G] SDF format, chain J [auth A] SDF format, chain S [auth D] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth F]	AA [auth G] BA [auth G] DA [auth H] EA [auth H] GA [auth I] AA [auth G], BA [auth G], DA [auth H], EA [auth H], GA [auth I], HA [auth I], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Y [auth F], Z [auth F]	methyl alpha-L-fucopyranoside C₇ H₁₄ O₅ OHWCAVRRXKJCRB-CXNFULCWSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain FA [auth H] SDF format, chain IA [auth I] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain CA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E]	CA [auth G] FA [auth H] IA [auth I] L [auth A] O [auth B] CA [auth G], FA [auth H], IA [auth I], L [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain IA [auth I] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.211
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.914	α = 90.04
b = 44.048	β = 91
c = 103.461	γ = 119.67

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2020-08-12
Changes: Database references, Structure summary
Version 1.3: 2020-12-16
Changes: Database references
Version 1.4: 2024-01-24
Changes: Data collection, Database references, Refinement description