8B87 | pdb_00008b87

Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide

PDB DOI: https://doi.org/10.2210/pdb8B87/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, Human papillomavirus 16
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-04 Released: 2023-10-18
Deposition Author(s): Stewart, B.Z., Kvansakul, M.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

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

Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide

Stewart, B.Z., Caria, S., Humbert, P.O., Kvansakul, M.

To be published.

Macromolecule Content

Total Structure Weight: 28.77 kDa
Atom Count: 1,715
Modeled Residue Count: 205
Deposited Residue Count: 260
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein scribble homolog	A, B	120	Homo sapiens	Mutation(s): 0 Gene Names: SCRIB, CRIB1, KIAA0147, LAP4, SCRB1, VARTUL
UniProt & NIH Common Fund Data Resources
Find proteins for Q14160 (Homo sapiens) Explore Q14160 Go to UniProtKB: Q14160
PHAROS: Q14160 GTEx: ENSG00000180900
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14160
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E6	C, D	10	Human papillomavirus 16	Mutation(s): 0
UniProt
Find proteins for P03126 (Human papillomavirus type 16) Explore P03126 Go to UniProtKB: P03126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03126
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SDY Query on SDY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	beta-D-talopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-QBFJYBIGSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]