5C6W | pdb_00005c6w

anti-CXCL13 scFv - E10

PDB DOI: https://doi.org/10.2210/pdb5C6W/pdb

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

Deposited: 2015-06-23 Released: 2015-11-04
Deposition Author(s): Tu, C., Bard, J., Mosyak, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.164 (Depositor), 0.166 (DCC)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair

Tu, C., Terraube, V., Tam, A., Stochaj, W., Fennell, B., Lin, L., Stahl, M., LaVallie, E., Somers, W., Finlay, W., Mosyak, L., Bard, J., Cunningham, O.

To be published.

Macromolecule Content

Total Structure Weight: 57.69 kDa
Atom Count: 4,436
Modeled Residue Count: 475
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84	A [auth H], B [auth J]	264	Homo sapiens	Mutation(s): 0 Gene Names: IGHV1-69-2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J2H0 (Homo sapiens) Explore A0A0B4J2H0 Go to UniProtKB: A0A0B4J2H0
GTEx: ENSG00000280411
Find proteins for P01704 (Homo sapiens) Explore P01704 Go to UniProtKB: P01704
GTEx: ENSG00000211666
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A0B4J2H0 P01704
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain RA [auth J] SDF format, chain Z [auth H] MOL2 format, chain RA [auth J] MOL2 format, chain Z [auth H] mmCIF format, chain RA [auth J] mmCIF format, chain Z [auth H]	RA [auth J], Z [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain RA [auth J] Focus chain Z [auth H] Interactions & Density Focus chain RA [auth J] Focus chain Z [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain DA [auth J] SDF format, chain EA [auth J] SDF format, chain G [auth H] SDF format, chain H MOL2 format, chain CA [auth J] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain G [auth H] MOL2 format, chain H mmCIF format, chain CA [auth J] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain G [auth H] mmCIF format, chain H	CA [auth J], DA [auth J], EA [auth J], G [auth H], H	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain G [auth H] Focus chain H Interactions & Density Focus chain CA [auth J] Focus chain DA [auth J] Focus chain EA [auth J] Focus chain G [auth H] Focus chain H
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain FA [auth J] SDF format, chain GA [auth J] SDF format, chain HA [auth J] SDF format, chain I [auth H] SDF format, chain IA [auth J] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain KA [auth J] SDF format, chain L [auth H] SDF format, chain LA [auth J] SDF format, chain M [auth H] SDF format, chain MA [auth J] SDF format, chain N [auth H] SDF format, chain NA [auth J] SDF format, chain O [auth H] SDF format, chain OA [auth J] SDF format, chain PA [auth J] SDF format, chain Q [auth H] SDF format, chain QA [auth J] SDF format, chain R [auth H] SDF format, chain S [auth H] SDF format, chain T [auth H] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Y [auth H] SDF format, chain P [auth H] SDF format, chain JA [auth J] MOL2 format, chain FA [auth J] MOL2 format, chain GA [auth J] MOL2 format, chain HA [auth J] MOL2 format, chain I [auth H] MOL2 format, chain IA [auth J] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain KA [auth J] MOL2 format, chain L [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth H] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth H] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth H] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth H] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain P [auth H] MOL2 format, chain JA [auth J] mmCIF format, chain FA [auth J] mmCIF format, chain GA [auth J] mmCIF format, chain HA [auth J] mmCIF format, chain I [auth H] mmCIF format, chain IA [auth J] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain KA [auth J] mmCIF format, chain L [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain M [auth H] mmCIF format, chain MA [auth J] mmCIF format, chain N [auth H] mmCIF format, chain NA [auth J] mmCIF format, chain O [auth H] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth H] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth H] mmCIF format, chain S [auth H] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain P [auth H] mmCIF format, chain JA [auth J]	FA [auth J] GA [auth J] HA [auth J] I [auth H] IA [auth J] FA [auth J], GA [auth J], HA [auth J], I [auth H], IA [auth J], J [auth H], JA [auth J], K [auth H], KA [auth J], L [auth H], LA [auth J], M [auth H], MA [auth J], N [auth H], NA [auth J], O [auth H], OA [auth J], P [auth H], PA [auth J], Q [auth H], QA [auth J], R [auth H], S [auth H], T [auth H], U [auth H], V [auth H], W [auth H], X [auth H], Y [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain I [auth H] Focus chain IA [auth J] Focus chain J [auth H] Focus chain JA [auth J] Focus chain K [auth H] Focus chain KA [auth J] Focus chain L [auth H] Focus chain LA [auth J] Focus chain M [auth H] Focus chain MA [auth J] Focus chain N [auth H] Focus chain NA [auth J] Focus chain O [auth H] Focus chain OA [auth J] Focus chain P [auth H] Focus chain PA [auth J] Focus chain Q [auth H] Focus chain QA [auth J] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain FA [auth J] Focus chain GA [auth J] Focus chain HA [auth J] Focus chain I [auth H] Focus chain IA [auth J] Focus chain J [auth H] Focus chain JA [auth J] Focus chain K [auth H] Focus chain KA [auth J] Focus chain L [auth H] Focus chain LA [auth J] Focus chain M [auth H] Focus chain MA [auth J] Focus chain N [auth H] Focus chain NA [auth J] Focus chain O [auth H] Focus chain OA [auth J] Focus chain P [auth H] Focus chain PA [auth J] Focus chain Q [auth H] Focus chain QA [auth J] Focus chain R [auth H] Focus chain S [auth H] Focus chain T [auth H] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain BA [auth J] MOL2 format, chain AA [auth J] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain BA [auth J] mmCIF format, chain AA [auth J] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain BA [auth J]	AA [auth J] BA [auth J] C [auth H] D [auth H] E [auth H] AA [auth J], BA [auth J], C [auth H], D [auth H], E [auth H], F [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.164 (Depositor), 0.166 (DCC)
R-Value Work: 0.154 (Depositor)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.98	α = 90
b = 80.36	β = 90
c = 119.24	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-11-04

Deposition Author(s):

Tu, C.

Bard, J.

Mosyak, L.

Revision History (Full details and data files)

Version 1.0: 2015-11-04
Type: Initial release
Version 1.1: 2017-11-01
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary