3TNN | pdb_00003tnn

Crystal structure of N5-i5 Fab, an ADCC mediating and non-neutralizing CD4i anti-HIV- 1 antibody.

PDB DOI: https://doi.org/10.2210/pdb3TNN/pdb

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

Deposited: 2011-09-01 Released: 2012-09-26
Deposition Author(s): Wu, X., Pazgier, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.245 (Depositor), 0.247 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of N5-i5 Fab, an ADCC and non-neutralizing anti-HIV-1 antibody

Guan, J., Wu, X., Pazgier, M., Lewis, G.

To be published.

Macromolecule Content

Total Structure Weight: 188.38 kDa
Atom Count: 13,429
Modeled Residue Count: 1,693
Deposited Residue Count: 1,772
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab heavy chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5	A [auth H], C [auth A], E [auth C], G [auth E]	226	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain of ADCC and non-neutralizing anti-HIV-1 antibody N5-i5	B [auth L], D [auth B], F [auth D], H [auth F]	217	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.245 (Depositor), 0.247 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.437	α = 90
b = 84.505	β = 101.08
c = 143.125	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Wu, X.

Pazgier, M.

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2021-04-21
Changes: Derived calculations, Source and taxonomy
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary