7RDW

Crystal Structure of FH1 Fab bound to HXb2 HIV-1 gp120 core

PDB DOI: https://doi.org/10.2210/pdb7RDW/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2021-07-12 Released: 2022-05-25
Deposition Author(s): Weidle, C., Pancera, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.55 Å
R-Value Free: 0.295
R-Value Work: 0.260
R-Value Observed: 0.262

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 365.29 kDa
Atom Count: 21,960
Modelled Residue Count: 2,973
Deposited Residue Count: 3,236
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 120	A [auth C], B [auth D], G [auth M], H [auth N]	373	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04578 Go to UniProtKB: P04578
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04578
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FH1 Fab Heavy Chain	C [auth G], K [auth U]	225	Homo sapiens	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FH1 Fab Heavy Chain	D [auth H], I [auth Q]	225	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
FH1 Fab Light Chain	E [auth I], F [auth L], J [auth R], L [auth V]	211	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: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth O], N [auth c], O [auth m], P [auth y]	3		N-Glycosylation	Interactions Focus chain M [auth O] Focus chain N [auth c] Focus chain O [auth m] Focus chain P [auth y] Interactions & Density Focus chain M [auth O] Focus chain N [auth c] Focus chain O [auth m] Focus chain P [auth y]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 S [auth C] SDF format, chain AB [auth N] SDF format, chain BB [auth N] SDF format, chain CA [auth D] SDF format, chain CB [auth N] SDF format, chain DA [auth D] SDF format, chain DB [auth N] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain NA [auth M] SDF format, chain OA [auth M] SDF format, chain PA [auth M] SDF format, chain Q [auth C] SDF format, chain QA [auth M] SDF format, chain R [auth C] SDF format, chain RA [auth M] SDF format, chain SA [auth M] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain UA [auth N] SDF format, chain V [auth C] SDF format, chain VA [auth N] SDF format, chain W [auth C] SDF format, chain WA [auth N] SDF format, chain XA [auth N] SDF format, chain YA [auth N] SDF format, chain ZA [auth N] MOL2 format, chain S [auth C] MOL2 format, chain AB [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth N] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth N] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain NA [auth M] MOL2 format, chain OA [auth M] MOL2 format, chain PA [auth M] MOL2 format, chain Q [auth C] MOL2 format, chain QA [auth M] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth M] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth N] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth N] MOL2 format, chain XA [auth N] MOL2 format, chain YA [auth N] MOL2 format, chain ZA [auth N]	AB [auth N] BB [auth N] CA [auth D] CB [auth N] DA [auth D] AB [auth N], BB [auth N], CA [auth D], CB [auth N], DA [auth D], DB [auth N], EA [auth D], FA [auth D], GA [auth D], NA [auth M], OA [auth M], PA [auth M], Q [auth C], QA [auth M], R [auth C], RA [auth M], S [auth C], SA [auth M], T [auth C], U [auth C], UA [auth N], V [auth C], VA [auth N], W [auth C], WA [auth N], XA [auth N], YA [auth N], ZA [auth N]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CA [auth D] Focus chain CB [auth N] Focus chain DA [auth D] Focus chain DB [auth N] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain NA [auth M] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain Q [auth C] Focus chain QA [auth M] Focus chain R [auth C] Focus chain RA [auth M] Focus chain S [auth C] Focus chain SA [auth M] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth N] Focus chain V [auth C] Focus chain VA [auth N] Focus chain W [auth C] Focus chain WA [auth N] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain ZA [auth N] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CA [auth D] Focus chain CB [auth N] Focus chain DA [auth D] Focus chain DB [auth N] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain NA [auth M] Focus chain OA [auth M] Focus chain PA [auth M] Focus chain Q [auth C] Focus chain QA [auth M] Focus chain R [auth C] Focus chain RA [auth M] Focus chain S [auth C] Focus chain SA [auth M] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth N] Focus chain V [auth C] Focus chain VA [auth N] Focus chain W [auth C] Focus chain WA [auth N] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain ZA [auth N]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain JA [auth D] SDF format, chain TA [auth M] MOL2 format, chain BA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain TA [auth M]	BA [auth C], JA [auth D], TA [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain TA [auth M] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain TA [auth M]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EB [auth N] SDF format, chain IA [auth D] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain EB [auth N] MOL2 format, chain IA [auth D] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain Z [auth C]	AA [auth C] EB [auth N] IA [auth D] KA [auth H] LA [auth H] AA [auth C], EB [auth N], IA [auth D], KA [auth H], LA [auth H], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EB [auth N] Focus chain IA [auth D] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EB [auth N] Focus chain IA [auth D] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain Z [auth C]
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain MA [auth I] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain MA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	HA [auth D], MA [auth I], X [auth C], Y [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain HA [auth D] Focus chain MA [auth I] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain HA [auth D] Focus chain MA [auth I] Focus chain X [auth C] Focus chain Y [auth C]