6WFV | pdb_00006wfv

The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human

PDB DOI: https://doi.org/10.2210/pdb6WFV/pdb

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

Deposited: 2020-04-04 Released: 2021-04-14
Deposition Author(s): Guo, H.-F., Tsai, C.-L., Miller, M.D., Phillips Jr., G.N., Tainer, J.A., Kurie, J.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.172 (Depositor), 0.176 (DCC)
R-Value Work:
0.152 (Depositor), 0.153 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of a collagen galactosylhydroxylysyl glucosyltransferase from human

Guo, H.-F., Tsai, C.-L., Miller, M.D., Phillips Jr., G.N., Tainer, J.A., Kurie, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 28.96 kDa
Atom Count: 2,191
Modeled Residue Count: 233
Deposited Residue Count: 247
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3	A	247	Homo sapiens	Mutation(s): 0 Gene Names: PLOD3 EC: 1.14.11.4 (PDB Primary Data), 2.4.1.50 (PDB Primary Data), 2.4.1.66 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60568 (Homo sapiens) Explore O60568 Go to UniProtKB: O60568
PHAROS: O60568 GTEx: ENSG00000106397
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60568
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.172 (Depositor), 0.176 (DCC)
R-Value Work: 0.152 (Depositor), 0.153 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.066	α = 90
b = 71.066	β = 90
c = 110.813	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	model building
SHELXE	model building
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA105155
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	K99CA225633
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP160652