3QEH | pdb_00003qeh

Crystal structure of human N12-i15, an ADCC and non-neutralizing anti-HIV-1 Env antibody

PDB DOI: https://doi.org/10.2210/pdb3QEH/pdb

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

Deposited: 2011-01-20 Released: 2012-01-25
Deposition Author(s): Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.254 (Depositor), 0.240 (DCC)
R-Value Work:
0.216 (Depositor), 0.200 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human N12-i15, an ADCC and non-neutralizing anti-HIV-1 Env antibody

Guan, Y., DeVico, A.L., Lewis, G.K., Pazgier, M.

To be published.

Macromolecule Content

Total Structure Weight: 196.53 kDa
Atom Count: 13,446
Modeled Residue Count: 1,670
Deposited Residue Count: 1,800
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of human anti-HIV-1 Env antibody N12-i15, heavy chain	A, C, E, G	232	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment of human anti-HIV-1 Env antibody N12-i15,light chain	B, D, F, H	218	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
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth E] SDF format, chain V [auth G] MOL2 format, chain I [auth A] MOL2 format, chain R [auth E] MOL2 format, chain V [auth G] mmCIF format, chain I [auth A] mmCIF format, chain R [auth E] mmCIF format, chain V [auth G]	I [auth A], R [auth E], V [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain R [auth E] Focus chain V [auth G] Interactions & Density Focus chain I [auth A] Focus chain R [auth E] Focus chain V [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain X [auth H] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain X [auth H] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain X [auth H]	P [auth D], S [auth E], T [auth F], X [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain X [auth H] Interactions & Density Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain X [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	J [auth A] K [auth B] L [auth B] M [auth B] N [auth C] J [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], Q [auth D], U [auth F], W [auth G], Y [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.254 (Depositor), 0.240 (DCC)
R-Value Work: 0.216 (Depositor), 0.200 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.121	α = 90
b = 125.121	β = 90
c = 149.902	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-10-09
Changes: Structure summary