5TLS

2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 and NAD

PDB DOI: https://doi.org/10.2210/pdb5TLS/pdb

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

Deposited: 2016-10-11 Released: 2016-10-26
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: 2.40 Å
R-Value Free: 0.187
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.4 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with DZ2002 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: 230.24 kDa
Atom Count: 17,156
Modelled Residue Count: 1,977
Deposited Residue Count: 1,992
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	498	Cryptosporidium parvum Iowa II	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C]	AA [auth D], E [auth A], M [auth B], S [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain S [auth C]
ZD2 Query on ZD2 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C]	BA [auth D], F [auth A], N [auth B], T [auth C]	(2S)-4-(6-amino-9H-purin-9-yl)-2-hydroxybutanoic acid C₉ H₁₁ N₅ O₃ NWPWVFAEENVVJM-YFKPBYRVSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain T [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [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 P [auth B] SDF format, chain Q [auth B] SDF format, chain R [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 CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [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 P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [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]	CA [auth D] DA [auth D] EA [auth D] FA [auth D] H [auth A] CA [auth D], DA [auth D], EA [auth D], FA [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [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 P [auth B] Focus chain Q [auth B] Focus chain R [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 CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [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 P [auth B] Focus chain Q [auth B] Focus chain R [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]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C]	O [auth B], U [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain O [auth B] Focus chain U [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.187
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m35tls

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.52	α = 90
b = 133.027	β = 90
c = 174.86	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description