1ONI | pdb_00001oni

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

PDB DOI: https://doi.org/10.2210/pdb1ONI/pdb

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-02-28 Released: 2003-04-08
Deposition Author(s): Manjasetty, B.A., Delbrueck, H., Mueller, U., Erdmann, M.F., Heinemann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.219 (DCC)
R-Value Work:
0.185 (Depositor), 0.189 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Homo sapiens protein hp14.5.

Manjasetty, B.A., Delbruck, H., Pham, D.T., Mueller, U., Fieber-Erdmann, M., Scheich, C., Sievert, V., Bussow, K., Niesen, F.H., Weihofen, W., Loll, B., Saenger, W., Heinemann, U., Neisen, F.H.

(2004) Proteins 54: 797-800

PubMed: 14997576 Search on PubMed
DOI: https://doi.org/10.1002/prot.10619
Primary Citation Related Structures:
1ONI

Organizational Affiliation

Protein Structure Factory, c/o BESSY GmbH, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 132.26 kDa
Atom Count: 9,553
Modeled Residue Count: 1,210
Deposited Residue Count: 1,242
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14.5 kDa translational inhibitor protein	A, B, C, D, E A, B, C, D, E, F, G, H, I	138	Homo sapiens	Mutation(s): 0 Gene Names: PSP EC: 3.5.99.10
UniProt & NIH Common Fund Data Resources
Find proteins for P52758 (Homo sapiens) Explore P52758 Go to UniProtKB: P52758
PHAROS: P52758 GTEx: ENSG00000132541
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52758
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] SDF format, chain U [auth I] SDF format, chain V [auth I] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth I] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth I]	J [auth A] K [auth A] L [auth B] M [auth B] N [auth C] J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth I]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth I] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth H] Focus chain U [auth I] Focus chain V [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.219 (DCC)
R-Value Work: 0.185 (Depositor), 0.189 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.158	α = 90
b = 154.158	β = 90
c = 104.559	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-04-08
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-11
Changes: Advisory, Refinement description
Version 1.4: 2024-02-14
Changes: Advisory, Data collection, Database references, Derived calculations

1ONI | pdb_00001oni

Crystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family

Literature

Crystal structure of Homo sapiens protein hp14.5.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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