12QD | pdb_000012qd

Crystal structure of CM12.1 Fab in complex with an orthomarburgvirus GP2 peptide

PDB DOI: https://doi.org/10.2210/pdb12QD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta, Orthomarburgvirus marburgense
Expression System: Macaca mulatta
Mutation(s): No

Deposited: 2026-04-14 Released: 2026-06-24
Deposition Author(s): Niyongabo, A., Janus, B.M., Ofek, G.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of CM12.1 Fab in complex with an orthomarburgvirus GP2 peptide

Niyongabo, A., Janus, B.M., Ofek, G.

To be published.

Macromolecule Content

Total Structure Weight: 98.83 kDa
Atom Count: 6,886
Modeled Residue Count: 890
Deposited Residue Count: 916
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CM12.1 Fab light chain	A [auth L], C [auth B]	218	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CM12.1 Fab heavy chain	B [auth H], D [auth A]	221	Macaca mulatta	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GP2 peptide	E [auth P], F [auth C]	19	Orthomarburgvirus marburgense	Mutation(s): 0
UniProt
Find proteins for Q1PDC7 (Lake Victoria marburgvirus (strain Ravn-87)) Explore Q1PDC7 Go to UniProtKB: Q1PDC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1PDC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	L [auth B], P [auth A], Q [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain L [auth B] Focus chain P [auth A] Focus chain Q [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain H SDF format, chain G [auth L] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain H MOL2 format, chain G [auth L] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain H mmCIF format, chain G [auth L]	G [auth L] H I [auth B] J [auth B] K [auth B] G [auth L], H, I [auth B], J [auth B], K [auth B], M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth L] Focus chain H Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain G [auth L] Focus chain H Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]