5I4F | pdb_00005i4f

scFv 2D10 complexed with alpha 1,6 mannobiose

PDB DOI: https://doi.org/10.2210/pdb5I4F/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-12 Released: 2016-12-21
Deposition Author(s): Vashisht, S., Kumar, A., Kaur, K.J., Salunke, D.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.193 (Depositor), 0.196 (DCC)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5VF2

Literature

Antibodies Can Exploit Molecular Crowding to Bind New Antigens at Noncanonical Paratope Positions

Vashisht, S., Kumar, A., Kaur, K.J., Salunke, D.M.

(2016) ChemistrySelect 1: 6287-6292

DOI: https://doi.org/10.1002/slct.201600945

Macromolecule Content

Total Structure Weight: 27.58 kDa
Atom Count: 2,189
Modeled Residue Count: 237
Deposited Residue Count: 251
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 2D10	A	251	Mus musculus	Mutation(s): 0

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	B, C	2		N/A	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G77384RA GlyCosmos: G77384RA GlyGen: G77384RA

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118 Query on PRD_900118	B, C	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.193 (Depositor), 0.196 (DCC)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.170 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.093	α = 90
b = 81.093	β = 90
c = 74.388	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-21
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary