3NA9 | pdb_00003na9

Crystal structure of Fab15

PDB DOI: https://doi.org/10.2210/pdb3NA9/pdb

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

Deposited: 2010-06-01 Released: 2010-08-18
Deposition Author(s): Luo, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.197 (Depositor), 0.190 (DCC)
R-Value Work:
0.168 (Depositor), 0.160 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Co-evolution of antibody stability and Vk CDR-L3 canonical structure

Luo, J., Feng, Y., Gilliland, G.L.

To be published.

Macromolecule Content

Total Structure Weight: 48.58 kDa
Atom Count: 3,937
Modeled Residue Count: 439
Deposited Residue Count: 439
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab15 light chain	A [auth L]	214	Homo sapiens	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
Fab15 heavy chain	B [auth H]	225	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth H] SDF format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain N [auth H]	N [auth H], O [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth H] Focus chain O [auth H] Interactions & Density Focus chain N [auth H] Focus chain O [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain J [auth H] SDF format, chain I [auth H] SDF format, chain H SDF format, chain E [auth L] SDF format, chain D [auth L] SDF format, chain C [auth L] MOL2 format, chain K [auth H] MOL2 format, chain J [auth H] MOL2 format, chain I [auth H] MOL2 format, chain H MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] MOL2 format, chain C [auth L] mmCIF format, chain K [auth H] mmCIF format, chain J [auth H] mmCIF format, chain I [auth H] mmCIF format, chain H 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] H I [auth H] C [auth L], D [auth L], E [auth L], H, I [auth H], J [auth H], K [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Interactions & Density Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain L [auth H] SDF format, chain G [auth L] SDF format, chain F [auth L] MOL2 format, chain M [auth H] MOL2 format, chain L [auth H] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] mmCIF format, chain M [auth H] mmCIF format, chain L [auth H] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L]	F [auth L], G [auth L], L [auth H], M [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth L] Focus chain G [auth L] Focus chain L [auth H] Focus chain M [auth H] Interactions & Density Focus chain F [auth L] Focus chain G [auth L] Focus chain L [auth H] Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.197 (Depositor), 0.190 (DCC)
R-Value Work: 0.168 (Depositor), 0.160 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.431	α = 90
b = 74.568	β = 103.32
c = 64.628	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-08-18

Deposition Author(s):

Luo, J.

Revision History (Full details and data files)

Version 1.0: 2010-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-03-31
Changes: Derived calculations, Source and taxonomy
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary