5F2Q | pdb_00005f2q

C-type lectin from Bothrops jararacussu

PDB DOI: https://doi.org/10.2210/pdb5F2Q/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bothrops jararacussu
Mutation(s): No

Deposited: 2015-12-02 Released: 2016-12-07
Deposition Author(s): de Padua, R.A.P., Pinheiro, M.P., Sartim, M.A., Sampaio, S.V., Nonato, M.C.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.265 (Depositor), 0.270 (DCC)
R-Value Work:
0.204 (Depositor), 0.200 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

C-type lectin from Bothrops jararacussu

de Padua, R.A.P., Pinheiro, M.P., Sartim, M.A., Vilela, S.S., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 161.72 kDa
Atom Count: 11,303
Modelled Residue Count: 1,344
Deposited Residue Count: 1,350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin BJcuL	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	135	Bothrops jararacussu	Mutation(s): 0
UniProt
Find proteins for P83519 (Bothrops jararacussu) Explore P83519 Go to UniProtKB: P83519
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P83519
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.265 (Depositor), 0.270 (DCC)
R-Value Work: 0.204 (Depositor), 0.200 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.25	α = 90
b = 115.15	β = 90
c = 156.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/11266-4
Sao Paulo Research Foundation (FAPESP)	Brazil	2011/23236-4

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2019-04-17
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary