6X5W | pdb_00006x5w

Peptide-bound structure of Marinomonas primoryensis peptide-binding domain

PDB DOI: https://doi.org/10.2210/pdb6X5W/pdb

Classification: PROTEIN BINDING
Organism(s): Marinomonas primoryensis, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-05-27 Released: 2021-09-01
Deposition Author(s): Guo, S., Davies, P.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Molecular basis for a bacterial adhesins peptide-binding module

Davies, P.L., Guo, S.

To be published.

Macromolecule Content

Total Structure Weight: 55.23 kDa
Atom Count: 4,463
Modeled Residue Count: 510
Deposited Residue Count: 511
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antifreeze protein	A	506	Marinomonas primoryensis	Mutation(s): 0
UniProt
Find proteins for A1YIY3 (Marinomonas primoryensis) Explore A1YIY3 Go to UniProtKB: A1YIY3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1YIY3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	B	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain AA [auth A]	AA [auth A], X [auth A], Y [auth A], Z [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] 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 A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] 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 A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A]	U [auth A], V [auth A], W [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]