4O9H | pdb_00004o9h

Structure of Interleukin-6 in complex with a Camelid Fab fragment

PDB DOI: https://doi.org/10.2210/pdb4O9H/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Mammalia
Mutation(s): No

Deposited: 2014-01-02 Released: 2015-04-15
Deposition Author(s): Klarenbeek, A., Blanchetot, C., Schragel, G., Sadi, A.S., Ongenae, N., Hemrika, W., Wijdenes, J., Spinelli, S., Desmyter, A., Cambillau, C., Hultberg, A., Kretz-rommel, A., Dreier, T., De haard, H.J.W., Roovers, R.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.244 (Depositor), 0.263 (DCC)
R-Value Work:
0.216 (Depositor), 0.227 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Combining residues of naturally-occurring Camelid somatic affinity variants yields ultra-potent human therapeutic IL-6 antibodies

Klarenbeek, A., Blanchetot, C., Schragel, G., Sadi, A.S., Ongenae, N., Hemrika, W., Wijdenes, J., Spinelli, S., Desmyter, A., Cambillau, C., Hultberg, A., Kretz-Rommel, A., Dreier, T., De haard, H.J.W., Roovers, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 67.17 kDa
Atom Count: 4,489
Modeled Residue Count: 563
Deposited Residue Count: 624
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-6	A	186	Homo sapiens	Mutation(s): 0 Gene Names: IL6, IFNB2
UniProt & NIH Common Fund Data Resources
Find proteins for P05231 (Homo sapiens) Explore P05231 Go to UniProtKB: P05231
PHAROS: P05231 GTEx: ENSG00000136244
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05231
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of the Camelid Fab fragment 61H7	B [auth H]	223	Lama glama	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of the Camelid Fab fragment 61H7	C [auth L]	215	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.244 (Depositor), 0.263 (DCC)
R-Value Work: 0.216 (Depositor), 0.227 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.21	α = 90
b = 47.47	β = 97
c = 148.32	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2015-04-29
Changes: Other
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary