5HM8

2.85 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenosine and NAD.

PDB DOI: https://doi.org/10.2210/pdb5HM8/pdb

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

Deposited: 2016-01-15 Released: 2016-01-27
Deposition Author(s): Minasov, G., Shuvalova, L., Halavaty, A., 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: 2.85 Å
R-Value Free: 0.200
R-Value Work: 0.173
R-Value Observed: 0.174

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.85 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenosine and NAD.

Minasov, G., Shuvalova, L., Halavaty, A., 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: 458.2 kDa
Atom Count: 32,193
Modelled Residue Count: 3,932
Deposited Residue Count: 3,984
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, E A, B, C, D, E, F, G, H	498	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd3_80 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
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 4 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 GA [auth E] SDF format, chain J [auth A] SDF format, chain KA [auth F] SDF format, chain OA [auth G] SDF format, chain P [auth B] SDF format, chain UA [auth H] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain UA [auth H] mmCIF format, chain V [auth C]	AA [auth D] GA [auth E] J [auth A] KA [auth F] OA [auth G] AA [auth D], GA [auth E], J [auth A], KA [auth F], OA [auth G], P [auth B], UA [auth H], V [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain KA [auth F] Focus chain OA [auth G] Focus chain P [auth B] Focus chain UA [auth H] Focus chain V [auth C]
ADN Query on ADN Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain I [auth A] SDF format, chain JA [auth F] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain TA [auth H] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	FA [auth E] I [auth A] JA [auth F] NA [auth G] O [auth B] FA [auth E], I [auth A], JA [auth F], NA [auth G], O [auth B], TA [auth H], U [auth C], Z [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain FA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain NA [auth G] Focus chain O [auth B] Focus chain TA [auth H] Focus chain U [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth E] SDF format, chain N [auth A] SDF format, chain SA [auth G] SDF format, chain T [auth B] SDF format, chain Y [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain IA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C]	IA [auth E], N [auth A], SA [auth G], T [auth B], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth E] Focus chain N [auth A] Focus chain SA [auth G] Focus chain T [auth B] Focus chain Y [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth F] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth G] SDF format, chain R [auth B] SDF format, chain RA [auth G] SDF format, chain S [auth B] SDF format, chain VA [auth H] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain VA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	BA [auth D] CA [auth D] DA [auth D] EA [auth D] HA [auth E] BA [auth D], CA [auth D], DA [auth D], EA [auth D], HA [auth E], K [auth A], L [auth A], LA [auth F], M [auth A], MA [auth F], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], S [auth B], VA [auth H], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain HA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain S [auth B] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.200
R-Value Work: 0.173
R-Value Observed: 0.174
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m35hm8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.837	α = 90
b = 185.31	β = 97.85
c = 122.439	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description