5BK3

Crystal structure of the neutralizing anti-circumsporozoite protein 580 antibody

PDB DOI: https://doi.org/10.2210/pdb5BK3/pdb

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

Deposited: 2017-09-12 Released: 2017-12-13
Deposition Author(s): Scally, S.W., Bosch, A., Triller, G., Wardemann, H., Julien, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.231
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 198.21 kDa
Atom Count: 13,490
Modelled Residue Count: 1,742
Deposited Residue Count: 1,792
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
580 Antibody, light chain	A [auth L], C [auth B], E [auth D], G [auth F]	220	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
580 Antibody, heavy chain	B [auth H], D [auth A], F [auth C], H [auth E]	228	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth G], J [auth I]	3		N-Glycosylation	Interactions Focus chain I [auth G] Focus chain J [auth I] Interactions & Density Focus chain I [auth G] Focus chain J [auth I]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	2		N-Glycosylation	Interactions Focus chain K [auth J] Interactions & Density Focus chain K [auth J]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L [auth K]	6		N-Glycosylation	Interactions Focus chain L [auth K] Interactions & Density Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain NA [auth C] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain QA [auth F] SDF format, chain T [auth H] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain QA [auth F] MOL2 format, chain T [auth H] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	DA [auth A] EA [auth A] IA [auth D] JA [auth D] NA [auth C] DA [auth A], EA [auth A], IA [auth D], JA [auth D], NA [auth C], P [auth L], Q [auth L], QA [auth F], T [auth H], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth A] Focus chain EA [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain NA [auth C] Focus chain P [auth L] Focus chain Q [auth L] Focus chain QA [auth F] Focus chain T [auth H] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain NA [auth C] Focus chain P [auth L] Focus chain Q [auth L] Focus chain QA [auth F] Focus chain T [auth H] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain M [auth L] SDF format, chain MA [auth C] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain R [auth H] SDF format, chain RA [auth E] SDF format, chain S [auth H] SDF format, chain SA [auth E] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth L] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth H] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B]	AA [auth A] BA [auth A] CA [auth A] FA [auth D] GA [auth D] AA [auth A], BA [auth A], CA [auth A], FA [auth D], GA [auth D], HA [auth D], KA [auth C], LA [auth C], M [auth L], MA [auth C], N [auth L], O [auth L], OA [auth F], PA [auth F], R [auth H], RA [auth E], S [auth H], SA [auth E], U [auth B], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth L] Focus chain MA [auth C] Focus chain N [auth L] Focus chain O [auth L] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth H] Focus chain RA [auth E] Focus chain S [auth H] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain M [auth L] Focus chain MA [auth C] Focus chain N [auth L] Focus chain O [auth L] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth H] Focus chain RA [auth E] Focus chain S [auth H] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.231
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.364	α = 90
b = 179.567	β = 109.61
c = 140.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SHELXPREP	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-12-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-13
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2020-02-26
Changes: Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary