5NJ9: Metalloprotease TldD

E. coli Microcin-processing metalloprotease TldD/E with DRVY angiotensin fragment bound. Determined by X-ray diffraction at 1.25 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 1.25 Å
Organisms: Escherichia coli K-12, Homo sapiens
Chains: 6
Atoms: 17,131
Mol. weight: 205.76 kDa
Ligands: ZN
Released: 4 Oct 2017

Explore 5NJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NJ9 contains 76 α-helices and 123 β-strands across 5 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.

Chains A and C: 22 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
α-helix	12-14	3
α-helix	18-29	12
β-strand	31	1	1
β-strand	35-51	17	2
β-strand	54-72	19	2
β-strand	75-81	7	2
α-helix	86-96	11
α-helix	97-99	3
β-strand	103	1	1
α-helix	108-111	4
β-strand	112	1	3
α-helix	131-148	18
β-strand	152-170	19	2
β-strand	174	1	3
β-strand	175-193	19	2
β-strand	196-206	11	2
α-helix	210-214	5
β-strand	216-217	2	4
β-strand	220-221	2	4
α-helix	222-239	18
β-strand	241	1	5
α-helix	242-244	3
β-strand	245-252	8	5
α-helix	253	1
α-helix	256-258	3
α-helix	259-261	3
α-helix	262-266	5
α-helix	267-269	3
β-strand	270	1	6
α-helix	271-276	6
β-strand	288	1	7
β-strand	296-299	4	7
β-strand	311	1	8
α-helix	316	1
β-strand	317	1	8
α-helix	318	1
β-strand	320-325	6	7
β-strand	328-329	2	7
β-strand	333	1	6
α-helix	336-342	7
β-strand	350-351	2	9
β-strand	360-361	2	9
β-strand	365-368	4	7
α-helix	369-370	2
β-strand	373	1	10
α-helix	375-380	6
β-strand	384-397	14	5
β-strand	402-414	13	5
β-strand	417-422	6	5
β-strand	426-430	5	5
α-helix	431-436	6
β-strand	438-441	4	5
β-strand	442	1	10
β-strand	446-447	2	7
β-strand	452-456	5	11
β-strand	459-463	5	11
β-strand	464-467	4	7
β-strand	470-478	9	5

Chain B: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	35-51	17	2
β-strand	54-72	19	2
β-strand	75-81	7	2
α-helix	86-100	15
α-helix	104-105	2
α-helix	112-113	2
α-helix	114-116	3
β-strand	117	1	12
α-helix	134-149	16
β-strand	155-174	20	2
β-strand	179-197	19	2
β-strand	200-210	11	2
α-helix	213-215	3
α-helix	217-218	2
α-helix	219-232	14
β-strand	237	1	13
α-helix	239-240	2
β-strand	242-248	7	13
α-helix	250-264	15
β-strand	265	1	14
α-helix	266-270	5
β-strand	283	1	15
β-strand	291-293	3	15
β-strand	311	1	12
α-helix	312-313	2
β-strand	316-320	5	15
β-strand	323-324	2	15
β-strand	328	1	14
α-helix	331-337	7
β-strand	351-352	2	15
α-helix	360-367	8
β-strand	370-377	8	13
β-strand	381	1	13
β-strand	387-398	12	13
β-strand	401-414	14	13
α-helix	415-420	6
β-strand	424-425	2	13
β-strand	435-436	2	15
β-strand	440-448	9	13

Chain D: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	10-30	21
β-strand	35-51	17	17
β-strand	54-72	19	17
β-strand	75-81	7	17
α-helix	86-100	15
α-helix	104-105	2
α-helix	112-113	2
α-helix	114-116	3
β-strand	117	1	27
α-helix	134-149	16
β-strand	155-174	20	17
β-strand	179-197	19	17
β-strand	200-210	11	17
α-helix	213-215	3
α-helix	217-218	2
α-helix	219-232	14
β-strand	237	1	28
α-helix	239-240	2
β-strand	242-248	7	28
α-helix	250-264	15
β-strand	265	1	29
α-helix	266-270	5
β-strand	283	1	30
β-strand	291-293	3	30
β-strand	311	1	27
α-helix	312-313	2
β-strand	316-320	5	30
β-strand	323-324	2	30
β-strand	328	1	29
α-helix	331-337	7
β-strand	351-352	2	30
α-helix	360-367	8
β-strand	370-377	8	28
β-strand	381	1	28
β-strand	387-398	12	28
β-strand	401-414	14	28
α-helix	415-420	6
β-strand	424-425	2	28
β-strand	435-436	2	30
β-strand	440-448	9	28

Chain E: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	603	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metalloprotease TldD	A, C	protein	495	Escherichia coli K-12	P0AGG8 (AlphaFold model)
Metalloprotease PmbA	B, D	protein	450	Escherichia coli K-12	P0AFK0 (AlphaFold model)
Asp-arg-val-tyr	E, F	protein	4	Homo sapiens	P01019 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5NJ9_1 Metalloprotease TldD (chains A, C)
MGSSHHHHHHSQDPMSLNLVSEQLLAANGLKHQDLFAILGQLAERRLDYGDLYFQSSYHE
SWVLEDRIIKDGSYNIDQGVGVRAISGEKTGFAYADQISLLALEQSAQAARTIVRDSGDG
KVQTLGAVEHSPLYTSVDPLQSMSREEKLDILRRVDKVAREADKRVQEVTASLSGVYELI
LVAATDGTLAADVRPLVRLSVSVLVEEDGKRERGASGGGGRFGYEFFLADLDGEVRADAW
AKEAVRMALVNLSAVAAPAGTMPVVLGAGWPGVLLHEAVGHGLEGDFNRRGTSVFSGQVG
ELVASELCTVVDDGTMVDRRGSVAIDDEGTPGQYNVLIENGILKGYMQDKLNARLMGMTP
TGNGRRESYAHLPMPRMTNTYMLPGKSTPQEIIESVEYGIYAPNFGGGQVDITSDKFVFS
TSEAYLIENGKVTKPVKGATLIGSGIETMQQISMVGNDLKLDNGVGVCGKEGQSLPVGVG
QPTLKVDNLTVGGTA

Sequence of entity 2 (B, D), FASTA

>5NJ9_2 Metalloprotease PmbA (chains B, D)
MALAMKVISQVEAQRKILEEAVSTALELASGKSDGAEVAVSKTTGISVSTRYGEVENVEF
NSDGALGITVYHQNRKGSASSTDLSPQAIARTVQAALDIARYTSPDPCAGVADKELLAFD
APDLDLFHPAEVSPDEAIELAARAEQAALQADKRITNTEGGSFNSHYGVKVFGNSHGMLQ
GYCSTRHSLSSCVIAEENGDMERDYAYTIGRAMSDLQTPEWVGADCARRTLSRLSPRKLS
TMKAPVIFANEVATGLFGHLVGAIAGGSVYRKSTFLLDSLGKQILPDWLTIEEHPHLLKG
LASTPFDSEGVRTERRDIIKDGILTQWLLTSYSARKLGLKSTGHAGGIHNWRIAGQGLSF
EQMLKEMGTGLVVTELMGQGVSAITGDYSRGAAGFWVENGEIQYPVSEITIAGNLKDMWR
NIVTVGNDIETRSNIQCGSVLLPEMKIAGQ

Sequence of entity 3 (E, F), FASTA

>5NJ9_3 ASP-ARG-VAL-TYR (chains E, F)
DRVY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (NA, EDO, MES) are not listed.

Primary citation

The Origins of Specificity in the Microcin-Processing Protease TldD/E. Ghilarov, D., Serebryakova, M., Stevenson, C.E.M. et al. Structure (2017) 25:1549-1561.e5. DOI 10.1016/j.str.2017.08.006 · PubMed

Other PDB entries of the same protein (UniProt P0AGG8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NJC 1.35 Å, E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide…
5NJA 1.4 Å, E. coli Microcin-processing metalloprotease TldD/E with angiotensin analogue bound
5NJF 1.42 Å, E. coli Microcin-processing metalloprotease TldD/E (TldD H262A mutant) with pentapeptide…
5NJB 1.5 Å, E. coli Microcin-processing metalloprotease TldD/E with actinonin bound
5NJ5 1.9 Å, E. coli Microcin-processing metalloprotease TldD/E with phosphate bound

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