2XSX | pdb_00002xsx

Crystal structure of human beta enolase ENOB

PDB DOI: https://doi.org/10.2210/pdb2XSX/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-09-30 Released: 2010-11-10
Deposition Author(s): Vollmar, M., Krysztofinska, E., Chaikuad, A., Krojer, T., Cocking, R., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.196 (DCC)
R-Value Work:
0.153 (Depositor), 0.161 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Beta Enolase Enob

Vollmar, M., Krysztofinska, E., Chaikuad, A., Krojer, T., Cocking, R., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Yue, W.W., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 95.58 kDa
Atom Count: 7,888
Modeled Residue Count: 869
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-ENOLASE	A, B	435	Homo sapiens	Mutation(s): 0 EC: 4.2.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P13929 (Homo sapiens) Explore P13929 Go to UniProtKB: P13929
PHAROS: P13929 GTEx: ENSG00000108515
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13929
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain D [auth A] MOL2 format, chain P [auth B] MOL2 format, chain D [auth A] mmCIF format, chain P [auth B] mmCIF format, chain D [auth A]	D [auth A], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] 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] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] 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] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] 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]	E [auth A] F [auth A] G [auth A] H [auth A] I [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], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain C [auth A] MOL2 format, chain O [auth B] MOL2 format, chain C [auth A] mmCIF format, chain O [auth B] mmCIF format, chain C [auth A]	C [auth A], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.189 (Depositor), 0.196 (DCC)
R-Value Work: 0.153 (Depositor), 0.161 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.878	α = 90
b = 105.531	β = 90
c = 106.091	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2012-12-05
Changes: Data collection, Database references, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description