5BQM: Botulinum neurotoxin type D

Crystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and targeted secretion inhibitor. Determined by X-ray diffraction at 3.1 Å resolution. Released 19 Aug 2015.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Clostridium botulinum, Homo sapiens
Chains: 4
Atoms: 13,263
Mol. weight: 210.92 kDa
Ligands: ZN
Released: 19 Aug 2015

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

Secondary structure: helices and β-sheets

5BQM contains 80 α-helices and 83 β-strands across 4 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: 19 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	19-23	5	1
β-strand	34-40	7	1
β-strand	43-45	3	1
β-strand	53	1	2
α-helix	60-61	2
β-strand	70	1	3
β-strand	72	1	4
α-helix	80-97	18
α-helix	101-112	12
α-helix	114-116	3
β-strand	126-128	3	5
β-strand	136-141	6	1
β-strand	146-152	7	1
β-strand	156-159	4	1
β-strand	164	1	4
α-helix	169-172	4
α-helix	179-183	5
β-strand	190-193	4	1
β-strand	198-203	6	6
β-strand	211	1	7
β-strand	215	1	7
β-strand	218-220	3	6
α-helix	223-238	16
α-helix	242-244	3
β-strand	248-249	2	8
β-strand	251	1	9
β-strand	265-266	2	8
α-helix	267-273	7
α-helix	275-280	6
α-helix	283-306	24
β-strand	309-311	3	5
α-helix	313-318	6
α-helix	319-330	12
β-strand	333-334	2	10
β-strand	340-341	2	10
α-helix	344-352	9
α-helix	353-357	5
α-helix	360-366	7
α-helix	377-379	3
β-strand	380-384	5	6
β-strand	394	1	11
β-strand	398	1	11
β-strand	414	1	6
β-strand	422-423	2	6
α-helix	424-425	2
β-strand	430	1	3
β-strand	433-437	5	12
β-strand	440	1	13

Chain B: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	511-512	2	14
β-strand	513	1	13
β-strand	517-520	4	12
β-strand	528	1	9
α-helix	536-538	3
β-strand	541-542	2	15
β-strand	578-579	2	1
α-helix	583-585	3
β-strand	591	1	2
α-helix	592-593	2
α-helix	595-598	4
β-strand	599-602	4	12
α-helix	608-615	8
α-helix	617-618	2
β-strand	625-627	3	16
α-helix	630-635	6
β-strand	639-641	3	16
α-helix	645-653	9
α-helix	660-675	16
β-strand	679	1	17
β-strand	690	1	17
α-helix	694-698	5
α-helix	709-716	8
α-helix	718-721	4
α-helix	725-728	4
α-helix	731-735	5
β-strand	736-737	2	15
α-helix	747-773	27
α-helix	774-778	5
α-helix	779-810	32
α-helix	816-852	37
α-helix	853-857	5
α-helix	858-882	25
α-helix	892-896	5
α-helix	897-899	3
α-helix	900-903	4

Chain C: 17 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	18
β-strand	34-40	7	18
β-strand	43-45	3	18
β-strand	53	1	19
α-helix	60-61	2
β-strand	70-71	2	20
α-helix	80-97	18
α-helix	101-112	12
α-helix	114-116	3
β-strand	126-128	3	21
β-strand	136-141	6	18
β-strand	146-152	7	18
β-strand	156-159	4	18
α-helix	180-183	4
β-strand	190-193	4	18
β-strand	198-201	4	22
β-strand	219	1	23
β-strand	220	1	22
α-helix	221-222	2
α-helix	223-239	17
α-helix	242-244	3
β-strand	248-249	2	24
β-strand	251	1	25
β-strand	265-266	2	24
α-helix	267-273	7
α-helix	275-280	6
α-helix	283-306	24
β-strand	309-311	3	21
α-helix	313-316	4
α-helix	319-330	12
β-strand	332-334	3	26
β-strand	340-342	3	26
α-helix	344-352	9
α-helix	353-357	5
α-helix	360-366	7
β-strand	380-384	5	22
β-strand	408	1	27
β-strand	410	1	27
β-strand	414	1	23
β-strand	422-423	2	22
α-helix	424-425	2
β-strand	429-430	2	20
β-strand	433-437	5	28
β-strand	440-443	4	29

Chain D: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	510-513	4	29
β-strand	517-520	4	28
α-helix	525-526	2
β-strand	528	1	25
α-helix	530-532	3
β-strand	541-542	2	30
β-strand	578-579	2	18
α-helix	583-585	3
β-strand	591	1	19
α-helix	592-593	2
β-strand	599-602	4	28
α-helix	608-615	8
α-helix	616-618	3
β-strand	625-627	3	31
α-helix	630-635	6
β-strand	639-641	3	31
α-helix	645-653	9
α-helix	660-675	16
β-strand	679-680	2	32
β-strand	689-690	2	32
α-helix	694-698	5
α-helix	709-716	8
α-helix	718-721	4
α-helix	725-728	4
α-helix	731-735	5
β-strand	736-737	2	30
α-helix	748-773	26
α-helix	774-778	5
α-helix	779-810	32
α-helix	820-852	33
α-helix	853-857	5
α-helix	858-882	25
α-helix	897-901	5
β-strand	909-910	2	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type D	A, C	protein	453	Clostridium botulinum	P19321
Somatoliberin,Botulinum neurotoxin type D	B, D	protein	474	Homo sapiens, Clostridium botulinum	P01286 (AlphaFold model), P19321

Sequence of entity 1 (A, C), FASTA

>5BQM_1 Botulinum neurotoxin type D (chains A, C)
MTWPVKDFNYSDPVNDNDILYLRIPQNKLITTPVKAFMITQNIWVIPERFSSDTNPSLSK
PPRPTSKYQSYYDPSYLSTDEQKDTFLKGIIKLFKRINERDIGKKLINYLVVGSPFMGDS
STPEDTFDFTRHTTNIAVEKFENGSWKVTNIITPSVLIFGPLPNILDYTASLTLQGQQSN
PSFEGFGTLSILKVAPEFLLTFSDVTSNQSSAVLGKSIFCMDPVIALMHELTHSLHQLYG
INIPSDKRIRPQVSEGFFSQDGPNVQFEELYTFGGLDVEIIPQIERSQLREKALGHYKDI
AKRLNNINKTIPSSWISNIDKYKKIFSEKYNFDKDNTGNFVVNIDKFNSLYSDLTNVMSE
VVYSSQYNVKNRTHYFSRHYLPVFANILDDNIYTIRDGFNLTNKGFNIENSGQNIERNPA
LQKLSSESVVDLFTKVCVDGIITSKTKSLIEGR

Sequence of entity 2 (B, D), FASTA

>5BQM_2 Somatoliberin,Botulinum neurotoxin type D (chains B, D)
HVDAIFTQSYRKVLAQLSARKLLQDILNRQQGERNQEQGALAGGGGSGGGGSGGGGSALV
LQCIKVKNNRLPYVADKDSISQEIFENKIITDETNVQNYSDKFSLDESILDGQVPINPEI
VDPLLPNVNMEPLNLPGEEIVFYDDITKYVDYLNSYYYLESQKLSNNVENITLTTSVEEA
LGYSNKIYTFLPSLAEKVNKGVQAGLFLNWANEVVEDFTTNIMKKDTLDKISDVSVIIPY
IGPALNIGNSALRGNFNQAFATAGVAFLLEGFPEFTIPALGVFTFYSSIQEREKIIKTIE
NCLEQRVKRWKDSYQWMVSNWLSRITTQFNHINYQMYDSLSYQADAIKAKIDLEYKKYSG
SDKENIKSQVENLKNSLDVKISEAMNNINKFIRECSVTYLFKNMLPKVIDELNKFDLRTK
TELINLIDSHNIILVGEVDRLKAKVNESFENTMPFNIFSYTNNSLLKDIINEYF

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors. Masuyer, G., Davies, J.R., Moore, K. et al. Sci Rep (2015) 5:13397-13397. DOI 10.1038/srep13397 · PubMed

Other PDB entries of the same protein (UniProt P19321), best resolution first:

2FPQ 1.65 Å, Crystal Structure of Botulinum Neurotoxin Type D Light Chain
3OGG 1.65 Å, Crystal structure of the receptor binding domain of botulinum neurotoxin D
3OBR 1.72 Å, Crystal structure of Botulinum neurotoxin serotype D binding domain
3N7J 2.0 Å, Crystal structure of botulinum neurotoxin serotype D binding domain
3OBT 2.0 Å, Crystal structure of Botulinum neurotoxin serotype D ligand binding domain in complex…
3RMY 2.3 Å, Crystal structure of HCR/D W1238A mutant
5BQN 2.3 Å, Crystal structure of the LHn fragment of botulinum neurotoxin type D, mutant H233Y E230Q
3RMX 2.75 Å, Crystal structure of HCR/D F1240A mutant

Browse structure collections

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