5V96 | pdb_00005v96

Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine

PDB DOI: https://doi.org/10.2210/pdb5V96/pdb

Classification: HYDROLASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-23 Released: 2017-05-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.180 (Depositor), 0.180 (DCC)
R-Value Work:
0.138 (Depositor), 0.139 (DCC)
R-Value Observed:
0.139 (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

Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 218.33 kDa
Atom Count: 16,616
Modeled Residue Count: 1,861
Deposited Residue Count: 1,920
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosyl-l-homocysteine Hydrolase	A, B, C, D	480	Naegleria fowleri	Mutation(s): 0 Gene Names: NF0035640 EC: 3.13.2.1
UniProt
Find proteins for A0A1Z0YU84 (Naegleria fowleri) Explore A0A1Z0YU84 Go to UniProtKB: A0A1Z0YU84
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Z0YU84
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 E [auth A] SDF format, chain HA [auth C] SDF format, chain VA [auth D] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain R [auth B]	E [auth A], HA [auth C], R [auth B], VA [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth C] Focus chain R [auth B] Focus chain VA [auth D] Interactions & Density Focus chain E [auth A] Focus chain HA [auth C] Focus chain R [auth B] Focus chain VA [auth D]
ADN Query on ADN Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain S [auth B] SDF format, chain WA [auth D] SDF format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain F [auth A]	F [auth A], IA [auth C], S [auth B], WA [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain IA [auth C] Focus chain S [auth B] Focus chain WA [auth D] Interactions & Density Focus chain F [auth A] Focus chain IA [auth C] Focus chain S [auth B] Focus chain WA [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain T [auth B] SDF format, chain XA [auth D] SDF format, chain G [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain G [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain G [auth A]	G [auth A], JA [auth C], T [auth B], XA [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain JA [auth C] Focus chain T [auth B] Focus chain XA [auth D] Interactions & Density Focus chain G [auth A] Focus chain JA [auth C] Focus chain T [auth B] Focus chain XA [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth D] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain FB [auth D] SDF format, chain GA [auth B] SDF format, chain GB [auth D] SDF format, chain H [auth A] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain KA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain V [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain UA [auth C] SDF format, chain U [auth B] SDF format, chain TA [auth C] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain JB [auth D] SDF format, chain I [auth A] SDF format, chain DB [auth D] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain DB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth D] mmCIF format, chain BB [auth D] mmCIF format, chain CB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain IB [auth D] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JB [auth D] mmCIF format, chain I [auth A] mmCIF format, chain DB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	AA [auth B] AB [auth D] BA [auth B] BB [auth D] CA [auth B] AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], FB [auth D], GA [auth B], GB [auth D], H [auth A], HB [auth D], I [auth A], IB [auth D], J [auth A], JB [auth D], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], W [auth B], X [auth B], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]