8BK2

X-ray structure of meningococcal factor H binding protein variant 2 in complex with a specific and bactericidal human monoclonal antibody 1B1

PDB DOI: https://doi.org/10.2210/pdb8BK2/pdb

Classification: PROTEIN BINDING
Organism(s): Neisseria meningitidis serogroup B, Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2022-11-08 Released: 2023-11-22
Deposition Author(s): Veggi, D., Bottomley, J.M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.270
R-Value Work: 0.204
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

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

Literature

Bactericidal human monoclonal antibody 1B1 specific for meningococcal factor H binding protein variant 2 and displaces human factor H

Veggi, D., Bottomley, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 228.07 kDa
Atom Count: 13,791
Modelled Residue Count: 1,798
Deposited Residue Count: 2,106
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Factor H-binding protein	A, B, C	260	Neisseria meningitidis serogroup B	Mutation(s): 0 Gene Names: fhbp
UniProt
Find proteins for C6JW56 (Neisseria meningitidis) Explore C6JW56 Go to UniProtKB: C6JW56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6JW56
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 Heavy chain	D [auth H], F [auth D], H [auth F]	226	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light Chains	E [auth L], G [auth E], I [auth G]	216	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain N [auth L] MOL2 format, chain N [auth L]	N [auth L]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain T [auth G] MOL2 format, chain T [auth G]	T [auth G]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain T [auth G] Interactions & Density Focus chain T [auth G]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain O [auth L] MOL2 format, chain O [auth L]	O [auth L]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain O [auth L] Interactions & Density Focus chain O [auth L]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C]	M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F]	J [auth A] K [auth B] P [auth D] Q [auth D] R [auth E] J [auth A], K [auth B], P [auth D], Q [auth D], R [auth E], S [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth F]