6E1X | pdb_00006e1x

Crystal structure of product-bound complex of spermidine/spermine N-acetyltransferase SpeG

PDB DOI: https://doi.org/10.2210/pdb6E1X/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-07-10 Released: 2019-07-10
Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.151 (Depositor), 0.150 (DCC)
R-Value Work:
0.123 (Depositor), 0.123 (DCC)
R-Value Observed:
0.125 (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 product-bound complex of spermidine/spermine N-acetyltransferase SpeG from Vibrio cholerae.

Filippova, E.V., Kiryukhina, O., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 129.18 kDa
Atom Count: 11,159
Modeled Residue Count: 1,027
Deposited Residue Count: 1,056
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N(1)-acetyltransferase	A, B, C, D, E A, B, C, D, E, F	176	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: speG, VC_A0947 EC: 2.3.1.57
UniProt
Find proteins for Q9KL03 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL03 Go to UniProtKB: Q9KL03
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KL03
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SP5 Query on SP5 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], V [auth D]	N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]acetamide C₁₂ H₂₈ N₄ O GUNURVWAJRRUAV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain V [auth D]
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain Z [auth E] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain K [auth B]	G [auth A] K [auth B] O [auth C] P [auth C] U [auth D] G [auth A], K [auth B], O [auth C], P [auth C], U [auth D], Z [auth E]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain Z [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain Z [auth E]
HLG Query on HLG Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	N-{3-[(4-aminobutyl)amino]propyl}acetamide C₉ H₂₁ N₃ O MQTAVJHICJWXBR-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B]	J [auth A], N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain M [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B]	M [auth B], T [auth C], Y [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain M [auth B] Focus chain T [auth C] Focus chain Y [auth D]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain R [auth C]	I [auth A], R [auth C], S [auth C], W [auth D], X [auth D]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C] Focus chain W [auth D] Focus chain X [auth D]