6GNK: Exoenzyme S from Pseudomonas aeruginosa

Name: PDB 6GNK: Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, trimeric crystal form bound to Carba-NAD
Published: 2018-09-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta, trimeric crystal form bound to Carba-NAD. Determined by X-ray diffraction at 2.55 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Homo sapiens, Pseudomonas aeruginosa
Chains: 3
Atoms: 5,282
Mol. weight: 83.15 kDa
Ligands: CNA
Released: 26 Sept 2018

Explore 6GNK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6GNK contains 35 α-helices and 8 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	21-33	13
α-helix	36-38	3
α-helix	40-70	31
α-helix	75-102	28
α-helix	103-107	5
α-helix	114-134	21
α-helix	138-161	24
α-helix	167-182	16
α-helix	187-203	17
α-helix	205-207	3
α-helix	213-231	19

Chain B: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	5-17	13
α-helix	21-33	13
α-helix	36-39	4
α-helix	40-70	31
α-helix	75-102	28
α-helix	103-107	5
α-helix	114-134	21
α-helix	138-161	24
α-helix	167-182	16
α-helix	187-203	17
α-helix	205-207	3
α-helix	213-230	18

Chain C: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	233-245	13
α-helix	247-250	4
α-helix	263-271	9
α-helix	272-276	5
α-helix	277-286	10
α-helix	288-291	4
α-helix	292-308	17
β-strand	315-321	7	1
β-strand	335-337	3	1
β-strand	342-345	4	1
α-helix	348-352	5
β-strand	358-364	7	1
β-strand	368-369	2	1
α-helix	376-378	3
β-strand	381-384	4	1
β-strand	389-397	9	1
β-strand	403-409	7	1
α-helix	410-412	3
α-helix	422-425	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
14-3-3 protein beta/alpha	A, B	protein	243	Homo sapiens	P31946 (AlphaFold model)
Exoenzyme S	C	protein	244	Pseudomonas aeruginosa	Q93SQ1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6GNK_1 14-3-3 protein beta/alpha (chains A, B)
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENENLYFQ
SLE

Sequence of entity 2 (C), FASTA

>6GNK_2 Exoenzyme S (chains C)
MGSSHHHHHHSQDPNSENLYFQGADKALADGLVKRFGADAEKYLGRQPGGIHSDAEVMAL
GLYTGIHYADLNRALRQGQELDAGQKLIDQGMSAAFEKSGQAEQVVKTFRGTRGGDAFNA
VEEGKVGHDDGYLSTSLNPGVARSFGQGTISTVFGRSGIDVSGISNYKNAKAILYNKETD
MRVLLSASDEQGVTRRVLEEAALGELSGHSQGLLDALDLASKPEPSGEVQEQDVRLRMRG
LDLA

Ligands and cofactors

ID	Name	Formula	Copies
CNA	Carba-nicotinamide-adenine-dinucleotide	C22 H30 N7 O13 P2	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface. Karlberg, T., Hornyak, P., Pinto, A.F. et al. Nat Commun (2018) 9:3785-3785. DOI 10.1038/s41467-018-06194-1 · PubMed

Other PDB entries of the same protein (UniProt P31946 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EQ8 1.5 Å, The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y130
5N10 1.6 Å, Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform
6HEP 1.86 Å, Crystal structure of human 14-3-3 beta in complex with CFTR R-domain peptide pS753-pS768
8EQH 1.9 Å, The crystal structure of 14-3-3 Beta containing 3-nitrotyrosine at position Y213
6A5Q 2.0 Å, Structure of 14-3-3 beta in complex with TFEB 14-3-3 binding motif
6YGJ 2.07 Å, small-molecule stabilizer of 14-3-3 and the Carbohydrate Response Element Binding…
4DNK 2.2 Å, Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation…
6GN8 2.34 Å, Exoenzyme S from Pseudomonas aeruginosa in complex with human 14-3-3 protein beta,…
2BQ0 2.5 Å, 14-3-3 Protein Beta (Human)
9GCP 2.59 Å, ChREBP/14-3-3 complex stabilized by AMP
2C23 2.65 Å, 14-3-3 Protein Beta (Human) in complex with exoenzyme S peptide
6BYK 3.0 Å, Structure of 14-3-3 beta/alpha bound to O-ClcNAc peptide

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