5T8K | pdb_00005t8k

1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD

PDB DOI: https://doi.org/10.2210/pdb5T8K/pdb

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

Deposited: 2016-09-07 Released: 2016-09-28
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: 1.95 Å
R-Value Free:
0.173 (Depositor), 0.179 (DCC)
R-Value Work:
0.141 (Depositor), 0.151 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine 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: 230.33 kDa
Atom Count: 18,512
Modeled Residue Count: 1,970
Deposited Residue Count: 1,992
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, D	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CPH1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	C	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 F [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Y [auth D]	F [auth A], L [auth B], R [auth C], Y [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain Y [auth D]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	H [auth A], N [auth B], T [auth C], U [auth C]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain U [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D]	AA [auth D], BA [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D]
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Z [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth D]	G [auth A], M [auth B], S [auth C], Z [auth D]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Z [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain O [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	CA [auth D], O [auth B], V [auth C], W [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B]	J [auth A], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain P [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain X [auth D]	E [auth A], K [auth B], Q [auth C], X [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain X [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	C	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.173 (Depositor), 0.179 (DCC)
R-Value Work: 0.141 (Depositor), 0.151 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.686	α = 90
b = 182.785	β = 100.58
c = 96.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary