9CFA | pdb_00009cfa

Germline-targeting HIV-1 gp120 engineered outer domain eODgt8 in complex with Fab eOD-CL04.1

PDB DOI: https://doi.org/10.2210/pdb9CFA/pdb

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

Deposited: 2024-06-27 Released: 2025-06-25
Deposition Author(s): Sarkar, A., Stanfield, R.L., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.224 (Depositor), 0.223 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Diverse competitor B cell responses to a germline-targeting priming immunogen in human Ig loci transgenic mice

Schiffner, T., Palser, A.

To be published.

Macromolecule Content

Total Structure Weight: 200.73 kDa
Atom Count: 13,622
Modeled Residue Count: 1,789
Deposited Residue Count: 1,851
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab eOD-CL04.1 lambda light chain	A [auth L], D [auth A], G [auth E]	215	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 eOD-CL04.1 heavy chain	B [auth H], E [auth B], H [auth F]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth H] Focus chain E [auth B] Focus chain H [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
germline-targeting HIV-1 gp120 engineered outer domain eODgt8	C, F [auth D], I [auth G]	183	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C Focus chain F [auth D] Focus chain I [auth G]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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 N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth F] SDF format, chain T [auth G] SDF format, chain U [auth G] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth F] MOL2 format, chain T [auth G] MOL2 format, chain U [auth G] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth F] mmCIF format, chain T [auth G] mmCIF format, chain U [auth G]	N [auth C] O [auth C] Q [auth D] R [auth D] S [auth F] N [auth C], O [auth C], Q [auth D], R [auth D], S [auth F], T [auth G], U [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth F] Focus chain T [auth G] Focus chain U [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L SDF format, chain M [auth L] SDF format, chain P [auth C] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain P [auth C] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain P [auth C]	L, M [auth L], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L Focus chain M [auth L] Focus chain P [auth C] Interactions & Density Focus chain L Focus chain M [auth L] Focus chain P [auth C]