4CT3

Methylmercury chloride derivative structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K

PDB DOI: https://doi.org/10.2210/pdb4CT3/pdb

Classification: VIRAL PROTEIN
Organism(s): Kayvirus kay
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-03-12 Released: 2014-08-06
Deposition Author(s): Sanz-Gaitero, M., Keary, R., Garcia-Doval, C., Coffey, A., van Raaij, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.224
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.

Sanz-Gaitero, M., Keary, R., Garcia-Doval, C., Coffey, A., van Raaij, M.J.

(2014) Virol J 11: 133-133

PubMed: 25064136 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/1743-422X-11-133
Primary Citation of Related Structures:
4CSH, 4CT3

PubMed Abstract:
Bacteriophages encode endolysins to lyse their host cell and allow escape of their progeny. Endolysins are also active against Gram-positive bacteria when applied from the outside and are thus attractive anti-bacterial agents. LysK, an endolysin from staphylococcal phage K, contains an N-terminal cysteine-histidine dependent amido-hydrolase/peptidase domain (CHAP(K)), a central amidase domain and a C-terminal SH3b cell wall-binding domain. CHAP(K) cleaves bacterial peptidoglycan between the tetra-peptide stem and the penta-glycine bridge.

Organizational Affiliation

Departamento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain. mjvanraaij@cnb.csic.es.

Macromolecule Content

Total Structure Weight: 80.08 kDa
Atom Count: 6,133
Modelled Residue Count: 652
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF30/ORF32	A, B, C, D	165	Kayvirus kay	Mutation(s): 0
UniProt
Find proteins for Q6Y7T6 (Staphylococcus phage K) Explore Q6Y7T6 Go to UniProtKB: Q6Y7T6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6Y7T6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMH Query on CMH Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C]	BA [auth D], E [auth A], N [auth B], V [auth C]	S-(METHYLMERCURY)-L-CYSTEINE C₄ H₉ Hg N O₂ S OMYFBIZVJYGJJA-JIZZDEOASA-M		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain V [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C]	DA [auth D], H [auth A], P [auth B], W [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain W [auth C]
MMC Query on MMC Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	FA [auth D] GA [auth D] J [auth A] K [auth A] R [auth B] FA [auth D], GA [auth D], J [auth A], K [auth A], R [auth B], S [auth B], Y [auth C], Z [auth C]	METHYL MERCURY ION C H₃ Hg DBUXSCUEGJMZAE-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
HG Query on HG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain HA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	AA [auth C] HA [auth D] L [auth A] M [auth A] T [auth B] AA [auth C], HA [auth D], L [auth A], M [auth A], T [auth B], U [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain HA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A]	CA [auth D], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain G [auth A] Interactions & Density Focus chain CA [auth D] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C]	EA [auth D], I [auth A], Q [auth B], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B]	F [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]