5GSM

Glycoside hydrolase B with product

PDB DOI: https://doi.org/10.2210/pdb5GSM/pdb

Classification: HYDROLASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-16 Released: 2017-02-01
Deposition Author(s): Watanabe, M., Kamachi, S., Mine, S.
Funding Organization(s): The Japan Society for the Promotion of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.175
R-Value Work: 0.130
R-Value Observed: 0.133

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Glycoside hydrolase B with product

Watanabe, M., Kamachi, S., Mine, S.

To be published.

Macromolecule Content

Total Structure Weight: 183.25 kDa
Atom Count: 14,357
Modelled Residue Count: 1,572
Deposited Residue Count: 1,572
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-beta-D-glucosaminidase	A, B	786	Thermococcus kodakarensis KOD1	Mutation(s): 0 Gene Names: Tk-Glm, TK1754
UniProt
Find proteins for Q76HN4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q76HN4 Go to UniProtKB: Q76HN4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76HN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
GCS Query on GCS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B]	C [auth A], N [auth B]	2-amino-2-deoxy-beta-D-glucopyranose C₆ H₁₃ N O₅ MSWZFWKMSRAUBD-QZABAPFNSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
PPI Query on PPI Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B]	J [auth A] K [auth A] L [auth A] U [auth B] V [auth B] J [auth A], K [auth A], L [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.175
R-Value Work: 0.130
R-Value Observed: 0.133
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.585	α = 90
b = 119.991	β = 98.66
c = 85.902	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-02-01

Deposition Author(s):

Watanabe, M.

Kamachi, S.

Mine, S.

Funding Organization	Location	Grant Number
The Japan Society for the Promotion of Sciences	Japan	25450143

Revision History (Full details and data files)

Version 1.0: 2017-02-01
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Structure summary