5BPK | pdb_00005bpk

Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases

PDB DOI: https://doi.org/10.2210/pdb5BPK/pdb

Classification: HYDROLASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-28 Released: 2016-05-18
Deposition Author(s): Bolz, C., Bach, N.C., Meyer, H., Mueller, G., Dawidowski, M., Popowicz, G., Sieber, S.A., Skerra, A., Gerhard, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.184 (Depositor), 0.191 (DCC)
R-Value Work:
0.144 (Depositor), 0.153 (DCC)
R-Value Observed:
0.145 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases

Bolz, C., Bach, N.C., Meyer, H., Mueller, G., Dawidowski, M., Popowicz, G., Sieber, S.A., Skerra, A., Gerhard, M.

To be published.

Macromolecule Content

Total Structure Weight: 133.74 kDa
Atom Count: 9,438
Modeled Residue Count: 1,072
Deposited Residue Count: 1,208
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyltranspeptidase (Ggt)	A, C [auth B]	379	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_1118 EC: 2.3.2.2 (UniProt), 3.4.19.13 (UniProt)
UniProt
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25743 Go to UniProtKB: O25743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25743
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyltranspeptidase (Ggt)	B [auth C], D	225	Helicobacter pylori 26695	Mutation(s): 0 Gene Names: HP_1118 EC: 2.3.2.2 (UniProt), 3.4.19.13 (UniProt)
UniProt
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25743 Go to UniProtKB: O25743
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O25743
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4UD Query on 4UD Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain MA [auth D] MOL2 format, chain O [auth C] MOL2 format, chain MA [auth D] mmCIF format, chain O [auth C] mmCIF format, chain MA [auth D]	MA [auth D], O [auth C]	(2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid C₅ H₈ N₂ O₃ CHVHVQLSTPEEOL-IMJSIDKUSA-N		Interactions Focus chain MA [auth D] Focus chain O [auth C] Interactions & Density Focus chain MA [auth D] Focus chain O [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain WA [auth D] SDF format, chain W [auth C] SDF format, chain VA [auth D] SDF format, chain V [auth C] SDF format, chain UA [auth D] SDF format, chain U [auth C] SDF format, chain TA [auth D] SDF format, chain T [auth C] SDF format, chain SA [auth D] SDF format, chain S [auth C] SDF format, chain RA [auth D] SDF format, chain R [auth C] SDF format, chain QA [auth D] SDF format, chain Q [auth C] SDF format, chain PA [auth D] SDF format, chain P [auth C] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain HA [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain R [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain P [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth D] mmCIF format, chain R [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain P [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], NA [auth D], OA [auth D], P [auth C], PA [auth D], Q [auth C], QA [auth D], R [auth C], RA [auth D], S [auth C], SA [auth D], T [auth C], TA [auth D], U [auth C], UA [auth D], V [auth C], VA [auth D], W [auth C], WA [auth D], X [auth C], Y [auth C], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth C] Focus chain PA [auth D] Focus chain Q [auth C] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth D] Focus chain S [auth C] Focus chain SA [auth D] Focus chain T [auth C] Focus chain TA [auth D] Focus chain U [auth C] Focus chain UA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain W [auth C] Focus chain WA [auth D] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain P [auth C] Focus chain PA [auth D] Focus chain Q [auth C] Focus chain QA [auth D] Focus chain R [auth C] Focus chain RA [auth D] Focus chain S [auth C] Focus chain SA [auth D] Focus chain T [auth C] Focus chain TA [auth D] Focus chain U [auth C] Focus chain UA [auth D] Focus chain V [auth C] Focus chain VA [auth D] Focus chain W [auth C] Focus chain WA [auth D] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.184 (Depositor), 0.191 (DCC)
R-Value Work: 0.144 (Depositor), 0.153 (DCC)
R-Value Observed: 0.145 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.777	α = 90
b = 112.006	β = 90.79
c = 91.854	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
XDS	data reduction
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-01
Changes: Advisory, Derived calculations, Structure summary