7X36 | pdb_00007x36

Crystal Structure of hetero-Diels-Alderase EupfF

PDB DOI: https://doi.org/10.2210/pdb7X36/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Penicillium janthinellum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-28 Released: 2023-04-05
Deposition Author(s): Zhou, J., Lu, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.245 (Depositor), 0.240 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Calcium-dependent glycosylated enzyme in the tandem hetero-Diels-Alder reaction

Zhou, J., Lu, J.

To be published.

Macromolecule Content

Total Structure Weight: 174.5 kDa
Atom Count: 12,420
Modeled Residue Count: 1,356
Deposited Residue Count: 1,492
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EupfF	A, B, C, D	373	Penicillium janthinellum	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YAC2 (Penicillium janthinellum) Explore A0A9Y2YAC2 Go to UniProtKB: A0A9Y2YAC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A9Y2YAC2
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, I, J E, F, H, I, J, K, N, O, P, Q	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain N Focus chain O Focus chain P Focus chain Q Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain N Focus chain O Focus chain P Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, M	3		N-Glycosylation	Interactions Focus chain G Focus chain M Interactions & Density Focus chain G Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C]	HA [auth C], IA [auth C], JA [auth C], R [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain R [auth A] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain R [auth A]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain RA [auth D] MOL2 format, chain RA [auth D] mmCIF format, chain RA [auth D]	RA [auth D]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain RA [auth D] Interactions & Density Focus chain RA [auth D]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain LA [auth C] SDF format, chain DA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain DA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain DA [auth B]	DA [auth B], LA [auth C], T [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain LA [auth C] Focus chain T [auth A] Interactions & Density Focus chain DA [auth B] Focus chain LA [auth C] Focus chain T [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain TA [auth D] SDF format, chain SA [auth D] SDF format, chain GA [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain GA [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain GA [auth B]	GA [auth B], SA [auth D], TA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Interactions & Density Focus chain GA [auth B] Focus chain SA [auth D] Focus chain TA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain PA [auth D] MOL2 format, chain PA [auth D] mmCIF format, chain PA [auth D]	PA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain PA [auth D] Interactions & Density Focus chain PA [auth D]
EDO Query on EDO 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 W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain QA [auth D] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain BA [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 W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain BA [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 W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] EA [auth B] FA [auth B] MA [auth C] AA [auth A], BA [auth A], EA [auth B], FA [auth B], MA [auth C], NA [auth C], QA [auth D], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain QA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [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 BA [auth A] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain QA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [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 S [auth A] SDF format, chain OA [auth D] SDF format, chain KA [auth C] SDF format, chain CA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain KA [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain KA [auth C] mmCIF format, chain CA [auth B]	CA [auth B], KA [auth C], OA [auth D], S [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain KA [auth C] Focus chain OA [auth D] Focus chain S [auth A] Interactions & Density Focus chain CA [auth B] Focus chain KA [auth C] Focus chain OA [auth D] Focus chain S [auth A]