4UDK

Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.76 Angstrom from unknown human gut bacteria (Uhgb_MP) in complex with N-acetyl-D-glucosamine, beta-D-mannopyranose and inorganic phosphate

PDB DOI: https://doi.org/10.2210/pdb4UDK/pdb

Classification: TRANSFERASE
Organism(s): uncultured organism
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-12-10 Released: 2015-05-27
Deposition Author(s): Ladeveze, S., Cioci, G., Potocki-Veronese, G., Tranier, S., Mourey, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.192
R-Value Work: 0.158
R-Value Observed: 0.160

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: 240.1 kDa
Atom Count: 17,398
Modelled Residue Count: 1,920
Deposited Residue Count: 2,082
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UHGB_MP	A, B, C, D, F	347	uncultured organism	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for D9ZDQ9 (uncultured organism) Explore D9ZDQ9 Go to UniProtKB: D9ZDQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D9ZDQ9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UHGB_MP	E	347	uncultured organism	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for D9ZDQ9 (uncultured organism) Explore D9ZDQ9 Go to UniProtKB: D9ZDQ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D9ZDQ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG Query on NDG Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain KA [auth F] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D]	EA [auth E] I [auth A] KA [auth F] O [auth B] T [auth C] EA [auth E], I [auth A], KA [auth F], O [auth B], T [auth C], Y [auth D]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain Y [auth D]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain H [auth A] SDF format, chain JA [auth F] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D]	DA [auth E] H [auth A] JA [auth F] N [auth B] S [auth C] DA [auth E], H [auth A], JA [auth F], N [auth B], S [auth C], X [auth D]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain DA [auth E] Focus chain H [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain DA [auth E] Focus chain H [auth A] Focus chain JA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain X [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain J [auth A] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain Z [auth D]	FA [auth E], J [auth A], Z [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain J [auth A] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain J [auth A] Focus chain Z [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain IA [auth F] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D]	CA [auth E] G [auth A] IA [auth F] M [auth B] R [auth C] CA [auth E], G [auth A], IA [auth F], M [auth B], R [auth C], W [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain CA [auth E] Focus chain G [auth A] Focus chain IA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C]	P [auth B], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain P [auth B] Focus chain U [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain LA [auth F] SDF format, chain NA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain NA [auth F]	AA [auth D], HA [auth E], K [auth A], LA [auth F], NA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain NA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain NA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain L [auth A] SDF format, chain MA [auth F] SDF format, chain Q [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C]	BA [auth D] GA [auth E] L [auth A] MA [auth F] Q [auth B] BA [auth D], GA [auth E], L [auth A], MA [auth F], Q [auth B], V [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain Q [auth B] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.192
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.737	α = 90
b = 140.886	β = 90
c = 168.831	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2015-06-17
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary