8CWJ

Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain (pRBD)

PDB DOI: https://doi.org/10.2210/pdb8CWJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Pangolin coronavirus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2022-05-19 Released: 2023-05-24
Deposition Author(s): Langley, D.B., Christ, D.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.230
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Neutralization of CoV-2 omicron lineages by affinity-matured class 5 antibodies

Langley, D.B., Christ, D.

To be published.

Macromolecule Content

Total Structure Weight: 242.85 kDa
Atom Count: 16,808
Modelled Residue Count: 2,121
Deposited Residue Count: 2,198
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of CR3022 antibody Fab	A [auth H], D [auth A]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of CR3022 antibody Fab	B [auth L], E [auth B]	220	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth G], F [auth I]	204	Pangolin coronavirus	Mutation(s): 0
UniProt
Find proteins for A0A7D6PMV8 (Pangolin coronavirus) Explore A0A7D6PMV8 Go to UniProtKB: A0A7D6PMV8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7D6PMV8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth G] Focus chain F [auth I]
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 4C12-B12 antibody Fab	G [auth J], I [auth U]	230	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 4C12-B12 antibody Fab	H [auth K], J [auth V]	215	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Oligosaccharides

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Entity ID: 6
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	K [auth C], L [auth D], M [auth E]	3		N-Glycosylation	Interactions Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Interactions & Density Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E]
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain P [auth G] MOL2 format, chain P [auth G] mmCIF format, chain P [auth G]	P [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth G] Interactions & Density Focus chain P [auth G]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain KA [auth V] SDF format, chain Q [auth G] SDF format, chain W [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth J] SDF format, chain GA [auth K] SDF format, chain IA [auth U] SDF format, chain LA [auth V] SDF format, chain MA [auth V] SDF format, chain N [auth H] SDF format, chain O [auth G] SDF format, chain U [auth I] SDF format, chain V [auth I] SDF format, chain X [auth I] SDF format, chain Y [auth I] MOL2 format, chain KA [auth V] MOL2 format, chain Q [auth G] MOL2 format, chain W [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth J] MOL2 format, chain GA [auth K] MOL2 format, chain IA [auth U] MOL2 format, chain LA [auth V] MOL2 format, chain MA [auth V] MOL2 format, chain N [auth H] MOL2 format, chain O [auth G] MOL2 format, chain U [auth I] MOL2 format, chain V [auth I] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth I] mmCIF format, chain KA [auth V] mmCIF format, chain Q [auth G] mmCIF format, chain W [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth J] mmCIF format, chain GA [auth K] mmCIF format, chain IA [auth U] mmCIF format, chain LA [auth V] mmCIF format, chain MA [auth V] mmCIF format, chain N [auth H] mmCIF format, chain O [auth G] mmCIF format, chain U [auth I] mmCIF format, chain V [auth I] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth I]	DA [auth J] EA [auth J] GA [auth K] IA [auth U] KA [auth V] DA [auth J], EA [auth J], GA [auth K], IA [auth U], KA [auth V], LA [auth V], MA [auth V], N [auth H], O [auth G], Q [auth G], U [auth I], V [auth I], W [auth I], X [auth I], Y [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth J] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth U] Focus chain KA [auth V] Focus chain LA [auth V] Focus chain MA [auth V] Focus chain N [auth H] Focus chain O [auth G] Focus chain Q [auth G] Focus chain U [auth I] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth I] Focus chain Y [auth I] Interactions & Density Focus chain DA [auth J] Focus chain EA [auth J] Focus chain GA [auth K] Focus chain IA [auth U] Focus chain KA [auth V] Focus chain LA [auth V] Focus chain MA [auth V] Focus chain N [auth H] Focus chain O [auth G] Focus chain Q [auth G] Focus chain U [auth I] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth I] Focus chain Y [auth I]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain AA [auth I] SDF format, chain CA [auth I] SDF format, chain FA [auth J] SDF format, chain HA [auth K] SDF format, chain JA [auth U] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain Z [auth I] MOL2 format, chain BA [auth I] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain HA [auth K] MOL2 format, chain JA [auth U] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain Z [auth I] mmCIF format, chain BA [auth I] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain HA [auth K] mmCIF format, chain JA [auth U] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth G] mmCIF format, chain Z [auth I]	AA [auth I] BA [auth I] CA [auth I] FA [auth J] HA [auth K] AA [auth I], BA [auth I], CA [auth I], FA [auth J], HA [auth K], JA [auth U], R [auth G], S [auth G], T [auth G], Z [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth U] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth U] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth G] Focus chain Z [auth I]