5UTU | pdb_00005utu

2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD

PDB DOI: https://doi.org/10.2210/pdb5UTU/pdb

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

Deposited: 2017-02-15 Released: 2017-03-01
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Stam, J., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.202 (Depositor), 0.195 (DCC)
R-Value Work:
0.170 (Depositor)
R-Value Observed:
0.172 (Depositor)

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

2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD

Minasov, G., Shuvalova, L., Dubrovska, I., Winsor, J., Stam, J., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 462.78 kDa
Atom Count: 33,201
Modeled Residue Count: 3,941
Deposited Residue Count: 3,984
Unique protein chains: 1

Macromolecules

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| 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% 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 HB [auth H] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain RA [auth F] SDF format, chain X [auth C] SDF format, chain YA [auth G] SDF format, chain LA [auth E] SDF format, chain EA [auth D] MOL2 format, chain HB [auth H] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain LA [auth E] MOL2 format, chain EA [auth D] mmCIF format, chain HB [auth H] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain YA [auth G] mmCIF format, chain LA [auth E] mmCIF format, chain EA [auth D]	EA [auth D] HB [auth H] I [auth A] LA [auth E] Q [auth B] EA [auth D], HB [auth H], I [auth A], LA [auth E], Q [auth B], RA [auth F], X [auth C], YA [auth G]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain EA [auth D] Focus chain HB [auth H] Focus chain I [auth A] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain X [auth C] Focus chain YA [auth G] Interactions & Density Focus chain EA [auth D] Focus chain HB [auth H] Focus chain I [auth A] Focus chain LA [auth E] Focus chain Q [auth B] Focus chain RA [auth F] Focus chain X [auth C] Focus chain YA [auth G]
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain ZA [auth G] SDF format, chain SA [auth F] SDF format, chain R [auth B] SDF format, chain MA [auth E] SDF format, chain J [auth A] SDF format, chain IB [auth H] SDF format, chain FA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain ZA [auth G] MOL2 format, chain SA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain MA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IB [auth H] MOL2 format, chain FA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain ZA [auth G] mmCIF format, chain SA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain MA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IB [auth H] mmCIF format, chain FA [auth D]	FA [auth D] IB [auth H] J [auth A] MA [auth E] R [auth B] FA [auth D], IB [auth H], J [auth A], MA [auth E], R [auth B], SA [auth F], Y [auth C], ZA [auth G]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain FA [auth D] Focus chain IB [auth H] Focus chain J [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain Y [auth C] Focus chain ZA [auth G] Interactions & Density Focus chain FA [auth D] Focus chain IB [auth H] Focus chain J [auth A] Focus chain MA [auth E] Focus chain R [auth B] Focus chain SA [auth F] Focus chain Y [auth C] Focus chain ZA [auth G]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain P [auth A] SDF format, chain NB [auth H] MOL2 format, chain W [auth B] MOL2 format, chain P [auth A] MOL2 format, chain NB [auth H] mmCIF format, chain W [auth B] mmCIF format, chain P [auth A] mmCIF format, chain NB [auth H]	NB [auth H], P [auth A], W [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain NB [auth H] Focus chain P [auth A] Focus chain W [auth B] Interactions & Density Focus chain NB [auth H] Focus chain P [auth A] Focus chain W [auth B]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain XA [auth F] SDF format, chain KA [auth D] MOL2 format, chain XA [auth F] MOL2 format, chain KA [auth D] mmCIF format, chain XA [auth F] mmCIF format, chain KA [auth D]	KA [auth D], XA [auth F]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain KA [auth D] Focus chain XA [auth F] Interactions & Density Focus chain KA [auth D] Focus chain XA [auth F]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain TA [auth F] SDF format, chain JB [auth H] MOL2 format, chain TA [auth F] MOL2 format, chain JB [auth H] mmCIF format, chain TA [auth F] mmCIF format, chain JB [auth H]	JB [auth H], TA [auth F]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain JB [auth H] Focus chain TA [auth F] Interactions & Density Focus chain JB [auth H] Focus chain TA [auth F]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain GB [auth G] SDF format, chain FB [auth G] MOL2 format, chain GB [auth G] MOL2 format, chain FB [auth G] mmCIF format, chain GB [auth G] mmCIF format, chain FB [auth G]	FB [auth G], GB [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FB [auth G] Focus chain GB [auth G] Interactions & Density Focus chain FB [auth G] Focus chain GB [auth G]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CB [auth G] SDF format, chain EB [auth G] SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MB [auth H] SDF format, chain O [auth A] SDF format, chain PA [auth E] SDF format, chain V [auth B] SDF format, chain VA [auth F] SDF format, chain WA [auth F] SDF format, chain U [auth B] SDF format, chain QA [auth E] SDF format, chain N [auth A] SDF format, chain LB [auth H] SDF format, chain IA [auth D] SDF format, chain DB [auth G] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain EB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth H] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain WA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain LB [auth H] MOL2 format, chain IA [auth D] MOL2 format, chain DB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain EB [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth H] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain WA [auth F] mmCIF format, chain U [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain LB [auth H] mmCIF format, chain IA [auth D] mmCIF format, chain DB [auth G] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	AA [auth C] BA [auth C] CA [auth C] CB [auth G] DA [auth C] AA [auth C], BA [auth C], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EB [auth G], HA [auth D], IA [auth D], JA [auth D], L [auth A], LB [auth H], M [auth A], MB [auth H], N [auth A], O [auth A], PA [auth E], QA [auth E], U [auth B], V [auth B], VA [auth F], WA [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain LB [auth H] Focus chain M [auth A] Focus chain MB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EB [auth G] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain L [auth A] Focus chain LB [auth H] Focus chain M [auth A] Focus chain MB [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain VA [auth F] Focus chain WA [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BB [auth G] SDF format, chain GA [auth D] SDF format, chain K [auth A] SDF format, chain NA [auth E] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] SDF format, chain UA [auth F] SDF format, chain OA [auth E] SDF format, chain KB [auth H] MOL2 format, chain AB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain UA [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain KB [auth H] mmCIF format, chain AB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain GA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain UA [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain KB [auth H]	AB [auth G] BB [auth G] GA [auth D] K [auth A] KB [auth H] AB [auth G], BB [auth G], GA [auth D], K [auth A], KB [auth H], NA [auth E], OA [auth E], S [auth B], T [auth B], UA [auth F], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth G] Focus chain BB [auth G] Focus chain GA [auth D] Focus chain K [auth A] Focus chain KB [auth H] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth G] Focus chain BB [auth G] Focus chain GA [auth D] Focus chain K [auth A] Focus chain KB [auth H] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain S [auth B] Focus chain T [auth B] Focus chain UA [auth F] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.202 (Depositor), 0.195 (DCC)
R-Value Work: 0.170 (Depositor)
R-Value Observed: 0.172 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.906	α = 90
b = 185.834	β = 97.98
c = 121.619	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

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Entry History

Deposition Data

Released Date: 2017-03-01

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2017-03-01
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary