2C4K | pdb_00002c4k

Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)

PDB DOI: https://doi.org/10.2210/pdb2C4K/pdb

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

Deposited: 2005-10-20 Released: 2005-10-24
Deposition Author(s): Kursula, P., Stenmark, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.299 (Depositor), 0.263 (DCC)
R-Value Work:
0.269 (Depositor)
R-Value Observed:
0.271 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Human Phosphoribosylpyrophosphate Synthetase-Associated Protein 39 (Pap39)

Kursula, P., Stenmark, P., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Ogg, D., Persson, C., Sagemark, J., Schuler, H., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Nordlund, P.

To be published.

Macromolecule Content

Total Structure Weight: 248.05 kDa
Atom Count: 14,378
Modeled Residue Count: 1,830
Deposited Residue Count: 2,220
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYL PYROPHOSPHATE SYNTHETASE-ASSOCIATED PROTEIN 1	A, B, C, D, E A, B, C, D, E, F	370	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14558 (Homo sapiens) Explore Q14558 Go to UniProtKB: Q14558
PHAROS: Q14558 GTEx: ENSG00000161542
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14558
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAM Query on TAM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain K [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D]	G [auth B] H [auth B] J [auth C] K [auth D] L [auth E] G [auth B], H [auth B], J [auth C], K [auth D], L [auth E], M [auth E], N [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.299 (Depositor), 0.263 (DCC)
R-Value Work: 0.269 (Depositor)
R-Value Observed: 0.271 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.055	α = 90
b = 103.875	β = 97.63
c = 127.161	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-10-24

Deposition Author(s):

Holmberg Schiavone, L.

Revision History (Full details and data files)

Version 1.0: 2005-10-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-01-17
Changes: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

2C4K | pdb_00002c4k

Crystal structure of human phosphoribosylpyrophosphate synthetase- associated protein 39 (PAP39)

Literature

Crystal Structure of Human Phosphoribosylpyrophosphate Synthetase-Associated Protein 39 (Pap39)

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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