6YMS

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

PDB DOI: https://doi.org/10.2210/pdb6YMS/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Geobacillus stearothermophilus
Mutation(s): No

Deposited: 2020-04-09 Released: 2021-04-21
Deposition Author(s): Kljajic, M., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.148
R-Value Work: 0.116
R-Value Observed: 0.117

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin

Kljajic, M., Gerber, H.-D., Heine, A., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 35.54 kDa
Atom Count: 2,959
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A [auth E]	316	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: nprS, nprM EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus) Explore P43133 Go to UniProtKB: P43133
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43133
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OZH (Subject of Investigation/LOI) Query on OZH Download Ideal Coordinates CCD File SDF format, chain J [auth E] MOL2 format, chain J [auth E] mmCIF format, chain J [auth E]	J [auth E]	(2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid C₂₄ H₃₂ N₃ O₇ P YJSHTZYDPJRJOL-UNMCSNQZSA-N		Interactions Focus chain J [auth E] Interactions & Density Focus chain J [auth E]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain K [auth E] MOL2 format, chain K [auth E] mmCIF format, chain K [auth E]	K [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth E] MOL2 format, chain L [auth E] mmCIF format, chain L [auth E]	L [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Interactions & Density Focus chain L [auth E]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain H [auth E] SDF format, chain I [auth E] MOL2 format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain I [auth E] mmCIF format, chain G [auth E] mmCIF format, chain H [auth E] mmCIF format, chain I [auth E]	G [auth E], H [auth E], I [auth E]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E] Interactions & Density Focus chain G [auth E] Focus chain H [auth E] Focus chain I [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth E] MOL2 format, chain F [auth E] mmCIF format, chain F [auth E]	F [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth E] Interactions & Density Focus chain F [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth E] SDF format, chain D [auth E] SDF format, chain E SDF format, chain B [auth E] MOL2 format, chain C [auth E] MOL2 format, chain D [auth E] MOL2 format, chain E MOL2 format, chain B [auth E] mmCIF format, chain C [auth E] mmCIF format, chain D [auth E] mmCIF format, chain E mmCIF format, chain B [auth E]	B [auth E], C [auth E], D [auth E], E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth E] Focus chain C [auth E] Focus chain D [auth E] Focus chain E Interactions & Density Focus chain B [auth E] Focus chain C [auth E] Focus chain D [auth E] Focus chain E