8FIF | pdb_00008fif

A2.3 Nanobody In Complex With Microcystin-LR

PDB DOI: https://doi.org/10.2210/pdb8FIF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Lama glama, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-12-16 Released: 2023-12-20
Deposition Author(s): Arenas, R., Tabares-da Rosa, S., Gonzalez-Sapienza, G., Wilson, D.K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.280 (Depositor), 0.282 (DCC)
R-Value Work:
0.236 (Depositor), 0.242 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

A2.3 Nanobody In Complex With Microcystin-LR

Arenas, R., Tabares-da Rosa, S., Gonzalez-Sapienza, G., Wilson, D.K.

To be published.

Macromolecule Content

Total Structure Weight: 46.1 kDa
Atom Count: 3,123
Modeled Residue Count: 379
Deposited Residue Count: 408
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single Domain Camelid Nanobody VHH A2.3	A, B, C	129	Lama glama	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcystin-LR	D, E [auth F], F [auth G]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1ZN Query on 1ZN	D, E [auth F], F [auth G]	PEPTIDE-LIKE	C₂₀ H₂₉ N O₃		--
DAL Query on DAL	D, E [auth F], F [auth G]	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MAA Query on MAA	D, E [auth F], F [auth G]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001031 Query on PRD_001031	D, E [auth F], F [auth G]	Microcystin-LR (MCLR) bound form	Oligopeptide / Toxin		Interactions Focus chain D Focus chain E [auth F] Focus chain F [auth G] Interactions & Density Focus chain D Focus chain E [auth F] Focus chain F [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.280 (Depositor), 0.282 (DCC)
R-Value Work: 0.236 (Depositor), 0.242 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.097	α = 90
b = 101.317	β = 90
c = 102.412	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-20

Deposition Author(s):

Tabares-da Rosa, S.

Gonzalez-Sapienza, G.

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2023-12-20
Type: Initial release
Version 1.1: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.