5I8O | pdb_00005i8o

HMM5 Fab in complex with disaccharide

• PDB DOI: https://doi.org/10.2210/pdb5I8O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-02-19 Released: 2016-03-23 
• Deposition Author(s): Andersen, G.R., Tjerrild, L.M., Spillner, E.
• Funding Organization(s): Novo Nordisk Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

Structure of HMM5 Fab with a bound disaccharide

Plum, M., Bantleon, F., Tjerrild, L., Raiber, T., Eckenberger, J., Wolf, S., Miehe, M., Jabs, F., Greunke, K., Seismann, H., Jakob, T., Andersen, G.R., Spillner, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 46.62 kDa 
• Atom Count: 3,940 
• Modeled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HMM5 antibody heavy chain	A [auth H]	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HMM5 antibody light chain	B [auth L]	217	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside	C [auth A]	2		N/A
Glycosylation Resources
GlyTouCan: G73237NF GlyCosmos: G73237NF

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.447	α = 90
b = 63.587	β = 90
c = 108.771	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Andersen, G.R., Tjerrild, L.M., Spillner, E.

---

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	--

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary