3AZV: Receptor binding domain

Name: PDB 3AZV: Crystal structure of the receptor binding domain
Published: 2011-12-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of the receptor binding domain. Determined by X-ray diffraction at 3.1 Å resolution. Released 28 Dec 2011.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 6,889
Mol. weight: 104.65 kDa
Released: 28 Dec 2011

Explore 3AZV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3AZV contains 21 α-helices and 71 β-strands across 2 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: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	859-866	8
β-strand	868-875	8	1
β-strand	878-881	4	1
β-strand	888-892	5	2
β-strand	896-897	2	1
β-strand	905-908	4	1
β-strand	916-920	5	2
α-helix	923-929	7
β-strand	933-943	11	1
α-helix	949-951	3
β-strand	952-958	7	2
β-strand	963-969	7	2
β-strand	972-978	7	2
β-strand	984-990	7	2
β-strand	1004-1011	8	1
β-strand	1015-1020	6	1
β-strand	1023-1029	7	1
α-helix	1030-1032	3
β-strand	1041-1048	8	2
β-strand	1063-1072	10	1
α-helix	1078-1087	10
β-strand	1093	1	3
β-strand	1095	1	4
β-strand	1101	1	4
α-helix	1102	1
β-strand	1103	1	5
β-strand	1107-1112	6	6
α-helix	1113-1115	3
β-strand	1118-1123	6	6
β-strand	1126-1131	6	6
β-strand	1144-1150	7	6
β-strand	1157	1	5
β-strand	1159	1	3
β-strand	1163-1169	7	6
β-strand	1174-1179	6	6
β-strand	1190-1192	3	7
β-strand	1193-1196	4	6
α-helix	1200-1206	7
β-strand	1209-1215	7	6
β-strand	1220-1226	7	6
β-strand	1227	1	8
β-strand	1234	1	8
β-strand	1236-1245	10	7
β-strand	1255-1264	10	7
α-helix	1270-1272	3
α-helix	1274-1276	3
β-strand	1278-1282	5	6

Chain B: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	859-866	8
β-strand	868-875	8	9
β-strand	878-881	4	9
β-strand	888-892	5	10
β-strand	897	1	9
β-strand	905-908	4	9
β-strand	916-920	5	10
α-helix	923-931	9
β-strand	934-942	9	9
α-helix	949-951	3
β-strand	952-958	7	10
β-strand	963-969	7	10
β-strand	972-978	7	10
β-strand	984-990	7	10
β-strand	1004-1010	7	9
β-strand	1016-1020	5	9
β-strand	1023-1028	6	9
α-helix	1037-1039	3
β-strand	1041-1048	8	10
α-helix	1049-1050	2
β-strand	1063-1072	10	9
α-helix	1078-1087	10
β-strand	1093	1	11
β-strand	1095	1	12
β-strand	1101	1	12
α-helix	1102	1
β-strand	1103	1	13
β-strand	1107-1112	6	14
α-helix	1113-1115	3
β-strand	1118-1123	6	14
β-strand	1126-1131	6	14
β-strand	1144-1148	5	14
β-strand	1157	1	13
β-strand	1159	1	11
β-strand	1163-1169	7	14
β-strand	1174-1179	6	14
β-strand	1190-1196	7	14
α-helix	1200-1206	7
β-strand	1209-1215	7	14
β-strand	1220-1228	9	14
β-strand	1231-1245	15	14
β-strand	1255-1263	9	14
α-helix	1270-1272	3
α-helix	1274-1276	3
β-strand	1278-1282	5	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
D/C mosaic neurotoxin	A, B	protein	443	Clostridium botulinum	Q9LBR1

Sequence of entity 1 (A, B), FASTA

>3AZV_1 D/C mosaic neurotoxin (chains A, B)
MEYFNNINEYFNSINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSS
GDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIIS
NFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKV
KELTGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQY
TNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIR
GNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFI
IQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASL
LESTSTHWVFVPASELEHHHHHH

Primary citation

Structural and mutational analyses of the receptor binding domain of botulinum D/C mosaic neurotoxin: insight into the ganglioside binding mechanism. Nuemket, N., Tanaka, Y., Tsukamoto, K. et al. Biochem Biophys Res Commun (2011) 411:433-439. DOI 10.1016/j.bbrc.2011.06.173 · PubMed

Other PDB entries of the same protein (UniProt Q9LBR1), best resolution first:

3N7L 2.0 Å, Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain
4ISR 2.59 Å, Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II
3N7M 2.6 Å, Crystal structure of W1252A mutant of HCR D/C VPI 5995
4ISQ 2.65 Å, Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
4FVV 2.7 Å, Crystal structure of HCR/D-Sa-GBL1/C
3AZW 2.99 Å, Crystal structure of the receptor binding domain

Browse structure collections

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