2BDZ

Mexicain from Jacaratia mexicana

PDB DOI: https://doi.org/10.2210/pdb2BDZ/pdb

Classification: HYDROLASE
Organism(s): Jacaratia mexicana
Mutation(s): No

Deposited: 2005-10-21 Released: 2006-10-03
Deposition Author(s): Gavira, J.A., Oliver-Salvador, M.C., Gonzalez-Ramirez, L.A., Soriano-Garcia, M., Garcia-Ruiz, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.238
R-Value Work: 0.177

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystallographic structure of Mexicain from Jacaratia mexicana

Gavira, J.A., Oliver-Salvador, M.C., Gonzalez-Ramirez, L.A., Soriano-Garcia, M., Garcia-Ruiz, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 96.62 kDa
Atom Count: 7,002
Modelled Residue Count: 848
Deposited Residue Count: 856
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mexicain	A, B, C, D	214	Jacaratia mexicana	Mutation(s): 0 EC: 3.4.22
UniProt
Find proteins for P84346 (Jacaratia mexicana) Explore P84346 Go to UniProtKB: P84346
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84346
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E64 Query on E64 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C₁₅ H₃₀ N₅ O₅ QPQNJAXBPHVASB-QWRGUYRKSA-O		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 ?
R-Value Free: 0.238
R-Value Work: 0.177
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 57.356	α = 90
b = 90.454	β = 92.636
c = 80.391	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-03

Deposition Author(s):

Gavira, J.A.

Oliver-Salvador, M.C.

Gonzalez-Ramirez, L.A.

Soriano-Garcia, M.

Garcia-Ruiz, J.M.

Revision History (Full details and data files)

Version 1.0: 2006-10-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

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Help and Resources

2BDZ

Mexicain from Jacaratia mexicana

Crystallographic structure of Mexicain from Jacaratia mexicana

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)