2YHX | pdb_00002yhx

SEQUENCING A PROTEIN BY X-RAY CRYSTALLOGRAPHY. II. REFINEMENT OF YEAST HEXOKINASE B CO-ORDINATES AND SEQUENCE AT 2.1 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb2YHX/pdb
Entry: 2YHX supersedes: 1YHX

Classification: TRANSFERASE(PHOSPHORYL,ALCOHOL ACCEPTOR)
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 1978-03-20 Released: 1978-05-23
Deposition Author(s): Steitz, T.A., Anderson, C.M., Stenkamp, R.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å

wwPDB Validation 3D Report Full Report

Validation slider image for 2YHX

This is version 1.4 of the entry. See complete history.

Literature

Sequencing a protein by x-ray crystallography. II. Refinement of yeast hexokinase B co-ordinates and sequence at 2.1 A resolution.

Anderson, C.M., Stenkamp, R.E., Steitz, T.A.

(1978) J Mol Biology 123: 15-33

PubMed: 355643 Search on PubMed
DOI: https://doi.org/10.1016/0022-2836(78)90374-1
Primary Citation Related Structures:
2YHX

Macromolecule Content

Total Structure Weight: 46.15 kDa
Atom Count: 3,311
Modeled Residue Count: 457
Deposited Residue Count: 457
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEXOKINASE B	A	457	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.1.1
UniProt
Find proteins for P04807 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04807 Go to UniProtKB: P04807
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04807
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OTG Query on OTG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-deoxy-2-{[(2-methylphenyl)carbonyl]amino}-alpha-D-glucopyranose C₁₄ H₁₉ N O₆ ZWRASUMSHKKCJN-SKENRDBWSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.5	α = 90
b = 59.2	β = 90
c = 58.5	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1978-05-23

Deposition Author(s):

This entry supersedes: 1YHX

Revision History (Full details and data files)

Version 1.0: 1978-05-23
Type: Initial release
Version 1.1: 2008-03-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Derived calculations, Other, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.