5VQM: Clostridium difficile TcdB-GTD

Clostridium difficile TcdB-GTD bound to PA41 Fab. Determined by X-ray diffraction at 2.79 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 2.79 Å
Organisms: Peptoclostridium difficile, Homo sapiens
Chains: 6
Atoms: 15,298
Mol. weight: 223.37 kDa
Released: 6 Dec 2017

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

Secondary structure: helices and β-sheets

5VQM contains 85 α-helices and 125 β-strands across 6 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: 32 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	22-34	13
α-helix	42-62	21
α-helix	69-89	21
β-strand	92-93	2	1
β-strand	97-101	5	2
α-helix	106-108	3
α-helix	109-120	12
β-strand	126-131	6	2
α-helix	138-155	18
α-helix	168-196	29
α-helix	202-213	12
α-helix	218-233	16
β-strand	237-239	3	2
α-helix	240-242	3
α-helix	244-248	5
α-helix	252-256	5
α-helix	257-261	5
α-helix	265-279	15
β-strand	282-285	4	2
β-strand	290	1	3
α-helix	291-292	2
β-strand	293	1	4
α-helix	294	1
α-helix	302-304	3
β-strand	307	1	5
α-helix	309-324	16
α-helix	335-337	3
β-strand	338	1	6
α-helix	340-352	13
α-helix	356-358	3
β-strand	360	1	4
β-strand	367-368	2	1
β-strand	374-378	5	2
β-strand	381-389	9	2
α-helix	394-418	25
α-helix	424-438	15
α-helix	444-448	5
α-helix	453-455	3
α-helix	465-468	4
α-helix	471-482	12
α-helix	495-498	4
α-helix	499-501	3
β-strand	502	1	2
α-helix	503-504	2
β-strand	509	1	3
α-helix	513-518	6

Chain B: 32 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	22-34	13
α-helix	42-62	21
α-helix	69-89	21
β-strand	92-93	2	19
β-strand	97-101	5	20
α-helix	106-108	3
α-helix	109-120	12
β-strand	126-131	6	20
α-helix	138-155	18
α-helix	168-196	29
α-helix	202-213	12
α-helix	218-233	16
β-strand	237-239	3	20
α-helix	240-242	3
α-helix	244-248	5
α-helix	252-256	5
α-helix	257-261	5
α-helix	265-279	15
β-strand	282-285	4	20
β-strand	290-291	2	21
α-helix	292	1
β-strand	293	1	22
α-helix	294	1
α-helix	302-304	3
β-strand	307	1	6
α-helix	309-324	16
α-helix	335-337	3
β-strand	338	1	5
α-helix	340-352	13
α-helix	356-358	3
β-strand	360	1	22
β-strand	367-368	2	19
β-strand	374-378	5	20
β-strand	381-389	9	20
α-helix	394-418	25
α-helix	424-438	15
α-helix	444-448	5
α-helix	453-455	3
α-helix	465-468	4
α-helix	471-482	12
α-helix	495-498	4
α-helix	499-501	3
β-strand	502	1	20
α-helix	503-504	2
β-strand	508-509	2	21
α-helix	513-518	6

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-13	4	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-46	2	24
β-strand	48-49	2	25
β-strand	53-54	2	25
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	85-90	6	24
β-strand	97-98	2	24
β-strand	102-106	5	24
α-helix	107	1
β-strand	111	1	26
β-strand	114-117	4	27
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	145-150	6	28
β-strand	153-155	3	28
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-182	10	27
α-helix	183-186	4
β-strand	192-197	6	28
β-strand	205-208	4	28

Chain D: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
α-helix	7-9	3
β-strand	10-12	3	24
β-strand	18-20	3	29
β-strand	22-25	4	29
α-helix	29-31	3
β-strand	33-39	7	24
β-strand	45-51	7	24
β-strand	58-60	3	24
β-strand	68-73	6	29
β-strand	78-83	6	29
α-helix	88-90	3
β-strand	92-99	8	24
β-strand	108-109	2	24
β-strand	113-117	5	24
β-strand	123	1	30
β-strand	126	1	31
β-strand	129	1	32
β-strand	142-146	5	32
β-strand	149-151	3	31
β-strand	152	1	30
β-strand	156	1	33
β-strand	159-160	2	33
β-strand	170-171	2	32
α-helix	172-174	3
β-strand	175-176	2	31
β-strand	182-183	2	31
β-strand	186-190	5	32
β-strand	201-206	6	33
β-strand	211-216	6	33

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-20	3	13
β-strand	22-25	4	13
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	108-109	2	14
β-strand	113-117	5	14
β-strand	123	1	15
α-helix	124-125	2
β-strand	126-128	3	16
β-strand	142-151	10	16
β-strand	152	1	15
β-strand	156	1	17
β-strand	170-171	2	16
α-helix	172-174	3
β-strand	175-176	2	16
β-strand	182-190	9	16
β-strand	201-203	3	18
β-strand	206	1	17
β-strand	211	1	17
β-strand	214-216	3	18

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
β-strand	45-48	4	8
β-strand	49	1	9
β-strand	53	1	9
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	98	1	8
β-strand	102-106	5	8
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-155	3	12
β-strand	159-160	2	11
β-strand	163	1	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	191-197	7	12
β-strand	205-210	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toxin B	A, B	protein	557	Peptoclostridium difficile	C9YJ35
PA41 FAB light chain	C, L	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)
PA41 FAB heavy chain	D, H	protein	222	Homo sapiens	S6B291 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VQM_1 Toxin B (chains A, B)
MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYI
DTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKD
VNSDYNVNVFYDSNAFLINTLKKTIVESATNDTLESFRENLNDPRFDYNKFYRKRMEIIY
DKQKNFINYYKTQREENPDLIIDDIVKIYLSNEYSKDIDELNSYIEESLNKVTENSGNDV
RNFEEFKGGESFKLYEQELVERWNLAAASDILRISALKEVGGVYLDVDMLPGIQPDLFES
IEKPSSVTVDFWEMVKLEAIMKYKEYIPGYTSEHFDMLDEEVQSSFESVLASKSDKSEIF
SSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLNPAISE
DNDFNTTTNAFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQD
LLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKKNYFE
GSLGHAGLRGSHHHHHH

Sequence of entity 2 (C, L), FASTA

>5VQM_2 PA41 FAB LIGHT CHAIN (chains C, L)
EIVLTQSPATLSLSPGERATLSCRASQSVGTSIHWYQQKPGQAPRLLIKFASESISGIPA
RFSGSGSGTDFTLTISSLEPEDFAVYYCQQSNKWPFTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, H), FASTA

>5VQM_3 PA41 FAB HEAVY CHAIN (chains D, H)
QVQLVQSGAEVKKPGASVKVSCKASGYPFTNYFMHWVRQAPGQRLEWIGRINPYNGATSY
SLNFRDKATITLDKSASTAYMELSSLRSEDTAVYYCARSTITSPLLDFWGQGTLVTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Primary citation

A neutralizing antibody that blocks delivery of the enzymatic cargo of Clostridium difficile toxin TcdB into host cells. Kroh, H.K., Chandrasekaran, R., Zhang, Z. et al. J Biol Chem (2018) 293:941-952. DOI 10.1074/jbc.M117.813428 · PubMed

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