4G6W | pdb_00004g6w

Human Thymidylate Synthase M190K with bound 4-Bromobenzene-1,2,3-triol

PDB DOI: https://doi.org/10.2210/pdb4G6W/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-07-19 Released: 2013-07-24
Deposition Author(s): Celeste, L.R., Lebioda, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.264 (Depositor), 0.255 (DCC)
R-Value Work:
0.222 (Depositor), 0.214 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Oxidation of Cysteine 195 of Huyman Thymidylate Synthase by Purpurogallin

Celeste, L.R., Lovelace, L.L., Lebioda, L.

To be published.

Macromolecule Content

Total Structure Weight: 36.27 kDa
Atom Count: 2,222
Modeled Residue Count: 270
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A [auth X]	313	Homo sapiens	Mutation(s): 1 Gene Names: tyms, ts, ok/sw-cl.29 EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens) Explore P04818 Go to UniProtKB: P04818
PHAROS: P04818 GTEx: ENSG00000176890
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04818
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PBX Query on PBX Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	4-bromobenzene-1,2,3-triol C₆ H₅ Br O₃ TYRFQQZIVRBJAK-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X]	C [auth X], D [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth X] Focus chain D [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A [auth X]	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
CSD Query on CSD	A [auth X]	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.264 (Depositor), 0.255 (DCC)
R-Value Work: 0.222 (Depositor), 0.214 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.846	α = 90
b = 95.846	β = 90
c = 80.525	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2014-11-19
Changes: Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: 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.