6XI2

Apo form of POMGNT2

PDB DOI: https://doi.org/10.2210/pdb6XI2/pdb

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

Deposited: 2020-06-19 Released: 2021-04-21
Deposition Author(s): Halmo, S.M., Yeh, J., Wells, L., Moremen, K.W., Lanzilotta, W.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.237
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 246.84 kDa
Atom Count: 17,188
Modelled Residue Count: 2,106
Deposited Residue Count: 2,142
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	A	533	Homo sapiens	Mutation(s): 0 Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens) Explore Q8NAT1 Go to UniProtKB: Q8NAT1
PHAROS: Q8NAT1 GTEx: ENSG00000144647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NAT1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	B	528	Homo sapiens	Mutation(s): 0 Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens) Explore Q8NAT1 Go to UniProtKB: Q8NAT1
PHAROS: Q8NAT1 GTEx: ENSG00000144647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NAT1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	C [auth D]	533	Homo sapiens	Mutation(s): 0 Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens) Explore Q8NAT1 Go to UniProtKB: Q8NAT1
PHAROS: Q8NAT1 GTEx: ENSG00000144647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NAT1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2	D [auth C]	528	Homo sapiens	Mutation(s): 0 Gene Names: POMGNT2, AGO61, C3orf39, EOGTL, GTDC2 EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens) Explore Q8NAT1 Go to UniProtKB: Q8NAT1
PHAROS: Q8NAT1 GTEx: ENSG00000144647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NAT1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA	E [auth G]	10	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-GLY-ALA-GLY-ALA-ALA-ALA-ALA-ALA-ALA	F [auth H]	10	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain W [auth D] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth D]	G [auth A], P [auth B], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth D]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] BA [auth D] CA [auth D] DA [auth C] EA [auth C] AA [auth D], BA [auth D], CA [auth D], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth D], Y [auth D], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]