8DF5

SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab

PDB DOI: https://doi.org/10.2210/pdb8DF5/pdb

Classification: VIRAL PROTEIN/Hydrolase/Immune System
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-06-21 Released: 2022-08-03
Deposition Author(s): McCallum, M., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Snell, G., Veesler, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.217
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 440.02 kDa
Atom Count: 26,905
Modelled Residue Count: 3,324
Deposited Residue Count: 3,900
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab Heavy Chain	A, C	230	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab Light Chain	B, D	214	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	E, F	805	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
PHAROS: Q9BYF1 GTEx: ENSG00000130234
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UniProt Group	Q9BYF1
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
S304 Fab Heavy Chain	G [auth H], I [auth M]	223	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
S304 Fab Light Chain	H [auth L], J [auth N]	215	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	K [auth R], L [auth S]	263	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
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UniProt Group	P0DTC2
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Reference Sequence

Oligosaccharides

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Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G], N [auth I]	2		N-Glycosylation	Interactions Focus chain M [auth G] Focus chain N [auth I] Interactions & Density Focus chain M [auth G] Focus chain N [auth I]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain MA [auth E] SDF format, chain WB [auth R] SDF format, chain XA [auth F] SDF format, chain ZA [auth F] SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain CB [auth F] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain YA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain WB [auth R] MOL2 format, chain XA [auth F] MOL2 format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain CB [auth F] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain YA [auth F]	AB [auth F] BB [auth F] CB [auth F] HA [auth E] IA [auth E] AB [auth F], BB [auth F], CB [auth F], HA [auth E], IA [auth E], JA [auth E], KA [auth E], LA [auth E], MA [auth E], WB [auth R], XA [auth F], YA [auth F], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain WB [auth R] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BB [auth F] Focus chain CB [auth F] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain WB [auth R] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain ZA [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain WA [auth F] SDF format, chain GA [auth E] MOL2 format, chain WA [auth F] MOL2 format, chain GA [auth E]	GA [auth E], WA [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain GA [auth E] Focus chain WA [auth F] Interactions & Density Focus chain GA [auth E] Focus chain WA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain DB [auth F] SDF format, chain EB [auth F] SDF format, chain GB [auth F] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain OB [auth L] SDF format, chain P [auth A] SDF format, chain PB [auth L] SDF format, chain TB [auth M] SDF format, chain VB [auth N] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XB [auth R] SDF format, chain YB [auth R] SDF format, chain Z [auth C] SDF format, chain BC [auth S] SDF format, chain CA [auth D] SDF format, chain FB [auth F] SDF format, chain NB [auth L] SDF format, chain O [auth A] SDF format, chain PA [auth E] SDF format, chain QA [auth E] SDF format, chain SB [auth M] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain UB [auth N] SDF format, chain V [auth B] SDF format, chain Y [auth B] SDF format, chain ZB [auth R] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth F] MOL2 format, chain EB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth L] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth L] MOL2 format, chain TB [auth M] MOL2 format, chain VB [auth N] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XB [auth R] MOL2 format, chain YB [auth R] MOL2 format, chain Z [auth C] MOL2 format, chain BC [auth S] MOL2 format, chain CA [auth D] MOL2 format, chain FB [auth F] MOL2 format, chain NB [auth L] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QA [auth E] MOL2 format, chain SB [auth M] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain UB [auth N] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain ZB [auth R]	BC [auth S] CA [auth D] DA [auth D] DB [auth F] EB [auth F] BC [auth S], CA [auth D], DA [auth D], DB [auth F], EB [auth F], FB [auth F], GB [auth F], NA [auth E], NB [auth L], O [auth A], OA [auth E], OB [auth L], P [auth A], PA [auth E], PB [auth L], QA [auth E], SB [auth M], T [auth B], TB [auth M], U [auth B], UB [auth N], V [auth B], VB [auth N], W [auth B], X [auth B], XB [auth R], Y [auth B], YB [auth R], Z [auth C], ZB [auth R]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BC [auth S] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain NA [auth E] Focus chain NB [auth L] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth L] Focus chain P [auth A] Focus chain PA [auth E] Focus chain PB [auth L] Focus chain QA [auth E] Focus chain SB [auth M] Focus chain T [auth B] Focus chain TB [auth M] Focus chain U [auth B] Focus chain UB [auth N] Focus chain V [auth B] Focus chain VB [auth N] Focus chain W [auth B] Focus chain X [auth B] Focus chain XB [auth R] Focus chain Y [auth B] Focus chain YB [auth R] Focus chain Z [auth C] Focus chain ZB [auth R] Interactions & Density Focus chain BC [auth S] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain NA [auth E] Focus chain NB [auth L] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth L] Focus chain P [auth A] Focus chain PA [auth E] Focus chain PB [auth L] Focus chain QA [auth E] Focus chain SB [auth M] Focus chain T [auth B] Focus chain TB [auth M] Focus chain U [auth B] Focus chain UB [auth N] Focus chain V [auth B] Focus chain VB [auth N] Focus chain W [auth B] Focus chain X [auth B] Focus chain XB [auth R] Focus chain Y [auth B] Focus chain YB [auth R] Focus chain Z [auth C] Focus chain ZB [auth R]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AC [auth R] SDF format, chain HB [auth F] SDF format, chain JB [auth F] SDF format, chain LB [auth F] SDF format, chain MB [auth H] SDF format, chain R [auth A] SDF format, chain RB [auth L] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain BA [auth C] SDF format, chain CC [auth S] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain IB [auth F] SDF format, chain KB [auth F] SDF format, chain Q [auth A] SDF format, chain QB [auth L] SDF format, chain RA [auth E] SDF format, chain S [auth A] SDF format, chain SA [auth E] MOL2 format, chain AA [auth C] MOL2 format, chain AC [auth R] MOL2 format, chain HB [auth F] MOL2 format, chain JB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth H] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth L] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CC [auth S] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain IB [auth F] MOL2 format, chain KB [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth L] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E]	AA [auth C] AC [auth R] BA [auth C] CC [auth S] EA [auth D] AA [auth C], AC [auth R], BA [auth C], CC [auth S], EA [auth D], FA [auth D], HB [auth F], IB [auth F], JB [auth F], KB [auth F], LB [auth F], MB [auth H], Q [auth A], QB [auth L], R [auth A], RA [auth E], RB [auth L], S [auth A], SA [auth E], TA [auth E], UA [auth E], VA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain AC [auth R] Focus chain BA [auth C] Focus chain CC [auth S] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth H] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth L] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Interactions & Density Focus chain AA [auth C] Focus chain AC [auth R] Focus chain BA [auth C] Focus chain CC [auth S] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain HB [auth F] Focus chain IB [auth F] Focus chain JB [auth F] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain MB [auth H] Focus chain Q [auth A] Focus chain QB [auth L] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth L] Focus chain S [auth A] Focus chain SA [auth E] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E]