3U79 | pdb_00003u79

AL-103 Y32F Y96F

PDB DOI: https://doi.org/10.2210/pdb3U79/pdb

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

Deposited: 2011-10-13 Released: 2012-07-04
Deposition Author(s): DiCostanzo, A.C., Thompson, J.R., Ramirez-Alvarado, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.223 (Depositor), 0.213 (DCC)
R-Value Work:
0.169 (Depositor)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Tyrosine Residues mediate crucial interactions in amyloid formation for immunoglobulin light chains

DiCostanzo, A.C., Thompson, J.R., Peterson, F.C., F Volkman, B., Ramirez-Alvarado, M.

To be published.

Macromolecule Content

Total Structure Weight: 99.25 kDa
Atom Count: 8,382
Modeled Residue Count: 885
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain	A, B, C, D, E A, B, C, D, E, F, G, H	111	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 BA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain BA [auth E]	BA [auth E]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Interactions & Density Focus chain BA [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] GA [auth H] HA [auth H] I [auth A] CA [auth F], FA [auth G], GA [auth H], HA [auth H], I [auth A], J [auth A], K [auth A], L [auth A], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], Z [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain Z [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] DA [auth F] EA [auth F] M [auth A] N [auth A] AA [auth E], DA [auth F], EA [auth F], M [auth A], N [auth A], Q [auth B], V [auth C], X [auth D], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.223 (Depositor), 0.213 (DCC)
R-Value Work: 0.169 (Depositor)
R-Value Observed: 0.169 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.02	α = 90
b = 128.02	β = 90
c = 98.84	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

DiCostanzo, A.C.

Thompson, J.R.

Ramirez-Alvarado, M.

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary