3QPQ

Crystal structure of ANTI-TLR3 antibody C1068 FAB

PDB DOI: https://doi.org/10.2210/pdb3QPQ/pdb

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

Deposited: 2011-02-14 Released: 2011-08-10
Deposition Author(s): Luo, J., Obmolova, G., Teplyakov, A., Gilliland, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.256
R-Value Work: 0.201
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Fab C1068

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

To be published.

Macromolecule Content

Total Structure Weight: 193.23 kDa
Atom Count: 15,233
Modelled Residue Count: 1,733
Deposited Residue Count: 1,752
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C1068 light chain	A [auth L], C [auth E], E [auth C], G [auth I]	215	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C1068 heavy chain	B [auth H], D [auth F], F [auth D], H [auth J]	223	Homo sapiens, Mus musculus This entity is chimeric	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L MOL2 format, chain L mmCIF format, chain L	L	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L Interactions & Density Focus chain L
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth I] SDF format, chain W [auth I] SDF format, chain X [auth J] SDF format, chain Y [auth J] SDF format, chain Z [auth J] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth I] MOL2 format, chain W [auth I] MOL2 format, chain X [auth J] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth J] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth I] mmCIF format, chain W [auth I] mmCIF format, chain X [auth J] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth J]	I [auth L] J [auth L] K [auth L] M [auth E] N [auth F] I [auth L], J [auth L], K [auth L], M [auth E], N [auth F], O [auth C], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth D], V [auth I], W [auth I], X [auth J], Y [auth J], Z [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth J] Focus chain Z [auth J]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.256
R-Value Work: 0.201
R-Value Observed: 0.204
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.48	α = 90
b = 136.94	β = 114.95
c = 83.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNX	refinement
StructureStudio	data collection
d*TREK	data reduction
d*TREK	data scaling
CNX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
Version 2.1: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary