1NKQ | pdb_00001nkq

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein

PDB DOI: https://doi.org/10.2210/pdb1NKQ/pdb

Classification: Structural Genomics, Unknown Function
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-01-03 Released: 2004-06-15
Deposition Author(s): Eswaramoorthy, S., Kumaran, D., Daniels, B., Studier, F.W., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.262 (Depositor)
R-Value Work:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crtystal Structure of Yeast Hypothetical Protein YNQ8_YEAST

Eswaramoorthy, S., Kumaran, D., Daniels, B., Studier, F.W., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 176.3 kDa
Atom Count: 12,088
Modelled Residue Count: 1,466
Deposited Residue Count: 1,554
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region	A, B, C, D, E A, B, C, D, E, F	259	Saccharomyces cerevisiae	Mutation(s): 6 Gene Names: YNL168C or N1696 EC: 5.3.2.2
UniProt
Find proteins for P53889 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53889 Go to UniProtKB: P53889
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53889
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth E]	H [auth A] I [auth A] L [auth B] N [auth B] O [auth B] H [auth A], I [auth A], L [auth B], N [auth B], O [auth B], S [auth C], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain Z [auth E]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] J [auth A] AA [auth E], BA [auth E], DA [auth F], EA [auth F], J [auth A], K [auth A], P [auth B], Q [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	CA [auth F] G [auth A] M [auth B] R [auth C] V [auth D] CA [auth F], G [auth A], M [auth B], R [auth C], V [auth D], Y [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain V [auth D] Focus chain Y [auth E]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.262 (Depositor)
R-Value Work: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.705	α = 90
b = 85.99	β = 90
c = 316.704	γ = 90

Software Package:

Software Name	Purpose
MARMAD	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SHARP	phasing
CNS	refinement
MARMAD	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-06-15

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-06-15
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-11-20
Changes: Data collection, Database references, Structure summary