4KQ3 | pdb_00004kq3

Crystal structure of Anti-IL-17A antibody CNTO3186

PDB DOI: https://doi.org/10.2210/pdb4KQ3/pdb

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

Deposited: 2013-05-14 Released: 2014-03-26
Deposition Author(s): Teplyakov, A., Obmolova, G., Malia, T., Gilliland, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.225 (Depositor), 0.209 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural evidence for a constrained conformation of short CDR-L3 in antibodies.

Teplyakov, A., Obmolova, G., Malia, T.J., Luo, J., Gilliland, G.L.

(2014) Proteins 82: 1679-1683

PubMed: 24470236 Search on PubMed
DOI: https://doi.org/10.1002/prot.24522
Primary Citation Related Structures:
4KQ3, 4KUZ

PubMed Abstract:
Three Fab structures used as targets in the Antibody Modeling Assessment presented a challenge for modeling CDR-L3 due to deviations from the most typical canonical structure. In all three antibodies CDR-L3 has eight residues, which is one residue shorter than usual, and has a conformation that is rarely observed in crystal structures. We analyzed the sequence and structural determinants of this conformation and found that the "short" CDR-L3 is remarkably rigid and retains the conformation in the interactions with antigens and neighboring CDRs.

Organizational Affiliation

Janssen Research & Development, LLC, Spring House, Pennsylvania, 19477.

Macromolecule Content

Total Structure Weight: 47.96 kDa
Atom Count: 3,624
Modeled Residue Count: 428
Deposited Residue Count: 439
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CNTO3186 light chain	A [auth L]	213	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CNTO3186 heavy chain	B [auth H]	226	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain D [auth L] SDF format, chain C [auth L] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] MOL2 format, chain C [auth L] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L] mmCIF format, chain C [auth L]	C [auth L], D [auth L], E [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Interactions & Density Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	B [auth H]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.225 (Depositor), 0.209 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.173 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.45	α = 90
b = 60.56	β = 99.66
c = 72.14	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
2CMR	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
2CMR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-26
Type: Initial release
Version 1.1: 2014-08-06
Changes: Database references
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
Version 2.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary