5YBY | pdb_00005yby

Structure of human Gliomedin

• PDB DOI: https://doi.org/10.2210/pdb5YBY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2017-09-05 Released: 2018-10-03 
• Deposition Author(s): Liu, H., Lin, Z., Xu, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

High resolution structure of human gliomedin

Liu, H., Lin, Z., Xu, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.79 kDa 
• Atom Count: 2,401 
• Modeled Residue Count: 245 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gliomedin	A	251	Homo sapiens	Mutation(s): 0  Gene Names: GLDN, COLM, UNQ9339/PRO34011
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZMI3 (Homo sapiens) Explore Q6ZMI3  Go to UniProtKB:  Q6ZMI3
PHAROS:  Q6ZMI3 GTEx:  ENSG00000186417
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q6ZMI3-1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	L [auth A], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	B [auth A], C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.88	α = 90
b = 81.573	β = 90
c = 66.194	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Liu, H., Lin, Z., Xu, F.

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-13
  Changes: Structure summary