4R4B

Crystal structure of the anti-hiv-1 antibody 2.2c

PDB DOI: https://doi.org/10.2210/pdb4R4B/pdb

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

Deposited: 2014-08-19 Released: 2014-09-10
Deposition Author(s): McLellan, J.S., Acharya, P., Huang, C.-C., Robinson, J., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.166
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 190.81 kDa
Atom Count: 14,523
Modelled Residue Count: 1,708
Deposited Residue Count: 1,720
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 2.2C LIGHT CHAIN	A [auth L], C [auth A], E [auth C], G [auth E]	210	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 2.2C HEAVY CHAIN	B [auth H], D [auth B], F [auth D], H [auth F]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain PA [auth F] SDF format, chain O [auth H] SDF format, chain Z [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain PA [auth F] MOL2 format, chain O [auth H] MOL2 format, chain Z [auth B]	LA [auth D], O [auth H], PA [auth F], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain LA [auth D] Focus chain O [auth H] Focus chain PA [auth F] Focus chain Z [auth B] Interactions & Density Focus chain LA [auth D] Focus chain O [auth H] Focus chain PA [auth F] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain I [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain Q [auth H] SDF format, chain QA [auth F] SDF format, chain R [auth H] SDF format, chain S [auth H] SDF format, chain SA [auth F] SDF format, chain U [auth A] SDF format, chain UA [auth F] SDF format, chain V [auth A] SDF format, chain Y [auth A] SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth C] SDF format, chain J [auth L] SDF format, chain JA [auth C] SDF format, chain K [auth L] SDF format, chain KA [auth C] SDF format, chain MA [auth D] SDF format, chain N [auth L] SDF format, chain P [auth H] SDF format, chain RA [auth F] SDF format, chain T [auth H] SDF format, chain TA [auth F] SDF format, chain VA [auth F] SDF format, chain W [auth A] SDF format, chain X [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain I [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth H] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth H] MOL2 format, chain S [auth H] MOL2 format, chain SA [auth F] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth F] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth L] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth L] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth L] MOL2 format, chain P [auth H] MOL2 format, chain RA [auth F] MOL2 format, chain T [auth H] MOL2 format, chain TA [auth F] MOL2 format, chain VA [auth F] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], I [auth L], IA [auth C], J [auth L], JA [auth C], K [auth L], KA [auth C], L, M [auth L], MA [auth D], N [auth L], NA [auth E], OA [auth E], P [auth H], Q [auth H], QA [auth F], R [auth H], RA [auth F], S [auth H], SA [auth F], T [auth H], TA [auth F], U [auth A], UA [auth F], V [auth A], VA [auth F], W [auth A], X [auth A], Y [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth L] Focus chain IA [auth C] Focus chain J [auth L] Focus chain JA [auth C] Focus chain K [auth L] Focus chain KA [auth C] Focus chain L Focus chain M [auth L] Focus chain MA [auth D] Focus chain N [auth L] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth H] Focus chain Q [auth H] Focus chain QA [auth F] Focus chain R [auth H] Focus chain RA [auth F] Focus chain S [auth H] Focus chain SA [auth F] Focus chain T [auth H] Focus chain TA [auth F] Focus chain U [auth A] Focus chain UA [auth F] Focus chain V [auth A] Focus chain VA [auth F] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain I [auth L] Focus chain IA [auth C] Focus chain J [auth L] Focus chain JA [auth C] Focus chain K [auth L] Focus chain KA [auth C] Focus chain L Focus chain M [auth L] Focus chain MA [auth D] Focus chain N [auth L] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth H] Focus chain Q [auth H] Focus chain QA [auth F] Focus chain R [auth H] Focus chain RA [auth F] Focus chain S [auth H] Focus chain SA [auth F] Focus chain T [auth H] Focus chain TA [auth F] Focus chain U [auth A] Focus chain UA [auth F] Focus chain V [auth A] Focus chain VA [auth F] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.214
R-Value Work: 0.166
R-Value Observed: 0.168
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.011	α = 90
b = 133.559	β = 91.36
c = 90.774	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2014-10-22
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-01-10
Changes: Derived calculations