5BPK

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
R-Value Work: 0.144
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

This is version 1.1 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
Modelled Residue Count: 1,072
Deposited Residue Count: 1,208
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 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
UniProt
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25743 Go to UniProtKB: O25743
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25743
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 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
UniProt
Find proteins for O25743 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25743 Go to UniProtKB: O25743
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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 MA [auth D] SDF format, chain O [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth C]	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 AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain P [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth C] SDF format, chain QA [auth D] SDF format, chain R [auth C] SDF format, chain RA [auth D] SDF format, chain S [auth C] SDF format, chain SA [auth D] SDF format, chain T [auth C] SDF format, chain TA [auth D] SDF format, chain U [auth C] SDF format, chain UA [auth D] SDF format, chain V [auth C] SDF format, chain VA [auth D] SDF format, chain W [auth C] SDF format, chain WA [auth D] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [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]