8DA0 | pdb_00008da0

Crystal structure of Mamba alpha-neurotoxin in complex with Centi-LNX-D09 antibody

PDB DOI: https://doi.org/10.2210/pdb8DA0/pdb

Classification: IMMUNE SYSTEM,ANTITOXIN/TOXIN
Organism(s): Homo sapiens, Dendraspis polylepis polylepis
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-06-12 Released: 2023-06-14
Deposition Author(s): Pletnev, S., Verardi, R., Tully, E.S., Glanville, J., Kwong, P.D.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.250 (DCC)
R-Value Work:
0.196 (Depositor), 0.203 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 3.0 of the entry. See complete history.

Literature

Venom protection by antibody from a snakebite hyperimmune subject

Glanville, J., Andrade, J., Bellin, M., Kim, S., Pletnev, S., Tsao, D., Verardi, R., Bedi, R., Friede, T., Tully, E., Zhang, B., Bylund, T., Liu, T., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 114.87 kDa
Atom Count: 8,031
Modelled Residue Count: 977
Deposited Residue Count: 1,046
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-LNX-D09 Fab light chain	A, C	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centi-LNX-D09 Fab heavy chain	B, D	237	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-elapitoxin-Dpp2d	E, F	72	Dendraspis polylepis polylepis	Mutation(s): 0
UniProt
Find proteins for C0HJD7 (Dendroaspis polylepis polylepis) Explore C0HJD7 Go to UniProtKB: C0HJD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0HJD7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain T [auth B]	AA [auth C], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain T [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	DA [auth D] EA [auth D] FA [auth D] G [auth A] GA [auth D] DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth B]	BA [auth C] CA [auth C] HA [auth D] IA [auth D] N [auth A] BA [auth C], CA [auth C], HA [auth D], IA [auth D], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.250 (DCC)
R-Value Work: 0.196 (Depositor), 0.203 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.703	α = 90
b = 145.537	β = 104.9
c = 64.207	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BALBES	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 2.0: 2024-09-04
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 3.0: 2024-10-09
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Atomic model, Data collection, Derived calculations, Structure summary