5A3L | pdb_00005a3l

Structure of Cea1A in complex with N-Acetylglucosamine

PDB DOI: https://doi.org/10.2210/pdb5A3L/pdb

Classification: CELL ADHESION
Organism(s): Komagataella pastoris DSMZ 70382
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2015-06-02 Released: 2016-06-29
Deposition Author(s): Kock, M., Brueckner, S., Wozniak, N., Veelders, M., Schlereth, J., Moesch, H.-U., Essen, L.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.202 (Depositor), 0.207 (DCC)
R-Value Work:
0.171 (Depositor), 0.179 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

High-Affinity Recognition of Non-Reducing Chitinous Ends by the Yeast Adhesin Cea1

Kock, M., Brueckner, S., Wozniak, N., Veelders, M., Schlereth, J., Moesch, H.-U., Essen, L.-O.

To be published.

Macromolecule Content

Total Structure Weight: 109.67 kDa
Atom Count: 7,992
Modeled Residue Count: 821
Deposited Residue Count: 960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CEA1	A, B, C, D	240	Komagataella pastoris DSMZ 70382	Mutation(s): 0
UniProt
Find proteins for A0A1A9TAD0 (Komagataella pastoris DSMZ 70382) Explore A0A1A9TAD0 Go to UniProtKB: A0A1A9TAD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1A9TAD0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG Query on NDG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	G [auth A], L [auth B], R [auth C], X [auth D]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain X [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D]	F [auth A], K [auth B], Q [auth C], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth D]	H [auth A], O [auth B], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain N [auth B]	N [auth B], S [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain N [auth B] Focus chain S [auth C] Focus chain Y [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D]	E [auth A], J [auth B], P [auth C], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain P [auth C] Focus chain V [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	AA [auth D], BA [auth D], I [auth A], T [auth C], U [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain T [auth C] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.202 (Depositor), 0.207 (DCC)
R-Value Work: 0.171 (Depositor), 0.179 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.34	α = 90
b = 106.21	β = 90
c = 107.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Experimental preparation, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary