5JPI

2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine and NAD

PDB DOI: https://doi.org/10.2210/pdb5JPI/pdb

Classification: HYDROLASE
Organism(s): Cryptosporidium parvum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-03 Released: 2016-05-18
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.181
R-Value Work: 0.142
R-Value Observed: 0.144

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2.15 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with D-Eritadenine and NAD.

Minasov, G., Shuvalova, L., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 229.82 kDa
Atom Count: 17,474
Modelled Residue Count: 1,970
Deposited Residue Count: 1,992
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	498	Cryptosporidium parvum	Mutation(s): 0 Gene Names: cgd3_80 EC: 3.3.1.1
UniProt
Find proteins for Q5CPH1 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CPH1 Go to UniProtKB: Q5CPH1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5CPH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Y [auth D]	E [auth A], I [auth B], P [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain Y [auth D]
DEA Query on DEA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain Z [auth D]	F [auth A], J [auth B], Q [auth C], Z [auth D]	D-ERITADENINE C₉ H₁₁ N₅ O₄ LIEMBEWXEZJEEZ-INEUFUBQSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain Z [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain BA [auth D] MOL2 format, chain BA [auth D]	BA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain BA [auth D] Interactions & Density Focus chain BA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain W [auth C] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain W [auth C]	M [auth B], S [auth C], W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth C] Interactions & Density Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C]	T [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain R [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C]	AA [auth D] G [auth A] H [auth A] K [auth B] L [auth B] AA [auth D], G [auth A], H [auth A], K [auth B], L [auth B], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain X [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain X [auth C]	CA [auth D], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain X [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	N [auth B], O [auth B], U [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.181
R-Value Work: 0.142
R-Value Observed: 0.144
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M35JPI

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.847	α = 90
b = 121.218	β = 90
c = 178.77	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2016-07-27
Changes: Other
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description