9GV9 | pdb_00009gv9

Structure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor and delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide

PDB DOI: https://doi.org/10.2210/pdb9GV9/pdb

Classification: LYASE
Organism(s): Bacteroides eggerthii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-23 Released: 2025-10-08
Deposition Author(s): Mycroft-West, C., Wu, L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.241 (Depositor), 0.205 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GV9

This is version 1.0 of the entry. See complete history.

Literature

Bacteroides eggerthii heparin lyase I liberates the rare delta-GlcA(alpha1->4)Glc3,6,N-sulphated disaccharide motif contained within the pentasaccharide of the clinical anticoagulant fondaparinux sodium

Kandola, T.K., Mycroft-West, C., Andrade De Lima, M.L., Turner, A., Gardini, C., Urso, E., Miller, G.J., Bisio, A., Yates, E.A., Guerrini, M., Wu, L., Skidmore, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 90.18 kDa
Atom Count: 6,647
Modeled Residue Count: 734
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparin lyase I	A [auth B], B [auth A]	382	Bacteroides eggerthii	Mutation(s): 0 Gene Names: HMPREF1016_01920
UniProt
Find proteins for E5WZ15 (Bacteroides eggerthii 1_2_48FAA) Explore E5WZ15 Go to UniProtKB: E5WZ15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5WZ15
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C [auth E], D [auth G]	2		N/A	Interactions Focus chain C [auth E] Focus chain D [auth G] Interactions & Density Focus chain C [auth E] Focus chain D [auth G]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth B] H [auth B] Q [auth A] E [auth B], F [auth B], G [auth B], H [auth B], Q [auth A], R [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain Q [auth A] Focus chain R [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain AA [auth A] MOL2 format, chain P [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain P [auth B] mmCIF format, chain AA [auth A]	AA [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain P [auth B] Interactions & Density Focus chain AA [auth A] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.241 (Depositor), 0.205 (DCC)
R-Value Work: 0.204 (Depositor), 0.205 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.59	α = 90
b = 91.563	β = 95.593
c = 73.443	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Mycroft-West, C.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	218579/Z/19/Z

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.