3I2B | pdb_00003i2b

The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase

PDB DOI: https://doi.org/10.2210/pdb3I2B/pdb

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

Deposited: 2009-06-29 Released: 2009-07-28
Deposition Author(s): Ugochukwu, E., Cocking, R., Pilka, E., Yue, W.W., Bray, J.E., Chaikuad, A., Krojer, T., Muniz, J., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.250 (DCC)
R-Value Work:
0.206 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of human 6 Pyruvoyl Tetrahydrobiopterin Synthase

Ugochukwu, E., Cocking, R., Pilka, E., Yue, W.W., Bray, J.E., Chaikuad, A., Krojer, T., Muniz, J., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 193.67 kDa
Atom Count: 13,128
Modeled Residue Count: 1,651
Deposited Residue Count: 1,692
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-pyruvoyl tetrahydrobiopterin synthase	A B [auth D] C [auth E] D [auth B] E [auth C] A, B [auth D], C [auth E], D [auth B], E [auth C], F, G, H, I, J, K, L	141	Homo sapiens	Mutation(s): 0 Gene Names: PTS EC: 4.2.3.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q03393 (Homo sapiens) Explore Q03393 Go to UniProtKB: Q03393
PHAROS: Q03393 GTEx: ENSG00000150787
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03393
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain Z [auth K] SDF format, chain Y [auth J] SDF format, chain X [auth I] SDF format, chain W [auth H] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain N [auth A] SDF format, chain BA [auth L] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain Z [auth K] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth I] MOL2 format, chain W [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth L] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain Z [auth K] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth I] mmCIF format, chain W [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth L]	BA [auth L] N [auth A] P [auth D] Q [auth E] S [auth B] BA [auth L], N [auth A], P [auth D], Q [auth E], S [auth B], T [auth C], U [auth F], V [auth G], W [auth H], X [auth I], Y [auth J], Z [auth K]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain BA [auth L] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K] Interactions & Density Focus chain BA [auth L] Focus chain N [auth A] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain O [auth A] MOL2 format, chain AA [auth K] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth K] mmCIF format, chain O [auth A]	AA [auth K], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain O [auth A] Interactions & Density Focus chain AA [auth K] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.250 (DCC)
R-Value Work: 0.206 (Depositor), 0.210 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.29	α = 90
b = 118.72	β = 90
c = 234.98	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description