5D1Z: IsdB NEAT1 bound by clone D4-10

IsdB NEAT1 bound by clone D4-10. Determined by X-ray diffraction at 3.17 Å resolution. Released 14 Sept 2016.

Method: X-ray diffraction
Resolution: 3.17 Å
Organisms: Homo sapiens, Staphylococcus aureus (strain MSSA476)
Chains: 10
Atoms: 15,704
Mol. weight: 245.42 kDa
Released: 14 Sept 2016

Explore 5D1Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D1Z contains 54 α-helices and 201 β-strands across 10 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	1
β-strand	12-15	4	2
β-strand	21-27	7	1
β-strand	35-40	6	2
β-strand	47-51	5	2
β-strand	55-56	2	2
β-strand	64-67	4	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	87-92	6	2
β-strand	100	1	2
β-strand	104-108	5	2
β-strand	113	1	3
α-helix	114-115	2
β-strand	116-120	5	4
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	4
β-strand	142	1	3
β-strand	147-152	6	5
β-strand	156	1	5
β-strand	161-165	5	4
α-helix	166-169	4
β-strand	175-184	10	4
α-helix	185-188	4
β-strand	193-199	7	5
α-helix	206	1
β-strand	207-212	6	5

Chain B: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
β-strand	11-13	3	7
β-strand	19-26	8	6
α-helix	30-32	3
β-strand	35-40	6	7
β-strand	46-52	7	7
β-strand	59-61	3	7
β-strand	69-74	6	6
β-strand	79-84	6	6
β-strand	93-100	8	7
β-strand	109-112	4	7
β-strand	117-120	4	7
α-helix	123-125	3
β-strand	126	1	8
α-helix	127-128	2
β-strand	129-133	5	9
β-strand	145-154	10	9
β-strand	155	1	8
β-strand	160-163	4	10
β-strand	172-174	3	9
α-helix	175-177	3
β-strand	178-179	2	9
β-strand	185-193	9	9
β-strand	203-208	6	10
β-strand	215-220	6	10

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	11
β-strand	11-15	5	12
β-strand	20-26	7	11
β-strand	34-39	6	12
β-strand	46-50	5	12
β-strand	54-55	2	12
α-helix	56	1
β-strand	63-64	2	11
β-strand	71-76	6	11
α-helix	81-83	3
β-strand	85-91	7	12
β-strand	99	1	12
β-strand	103-108	6	12
β-strand	112	1	13
α-helix	113-115	3
β-strand	116-119	4	14
α-helix	120-122	3
β-strand	132-140	9	14
β-strand	141	1	13
β-strand	146-149	4	15
β-strand	160-164	5	14
α-helix	165-168	4
β-strand	174-181	8	14
α-helix	184-188	5
β-strand	192-198	7	15
β-strand	206-211	6	15

Chain D: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	16
β-strand	11-12	2	17
β-strand	18-23	6	16
β-strand	35-41	7	18
β-strand	47-54	8	18
β-strand	59-61	3	18
β-strand	69-70	2	16
β-strand	73-74	2	16
β-strand	79-84	6	16
α-helix	89-91	3
β-strand	93-100	8	18
β-strand	115-118	4	18
β-strand	123-124	2	18
β-strand	125-126	2	17
α-helix	129-131	3
β-strand	132	1	19
α-helix	133-134	2
β-strand	135-139	5	20
β-strand	150-160	11	20
β-strand	161	1	19
β-strand	166-167	2	21
β-strand	178-180	3	20
α-helix	181-183	3
β-strand	184-185	2	20
β-strand	191-200	10	20
β-strand	210	1	22
β-strand	213-215	3	21
α-helix	216-218	3
β-strand	220-222	3	21
β-strand	225	1	22

Chain E: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	26
β-strand	12-16	5	27
β-strand	21-27	7	26
β-strand	35-40	6	27
β-strand	47-51	5	27
β-strand	55-56	2	27
α-helix	57	1
β-strand	64-66	3	26
β-strand	72-77	6	26
α-helix	82-84	3
β-strand	86-92	7	27
β-strand	100	1	27
β-strand	105-109	5	27
β-strand	113	1	28
α-helix	114-116	3
β-strand	117-119	3	29
α-helix	121-123	3
α-helix	125-127	3
β-strand	131-141	11	29
β-strand	142	1	28
β-strand	147-152	6	30
β-strand	162-165	4	29
α-helix	166-169	4
β-strand	175-184	10	29
α-helix	185-188	4
β-strand	194-199	6	30
β-strand	207-210	4	30

Chain F: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	11-12	2	32
β-strand	18-24	7	31
β-strand	35-41	7	33
β-strand	47-54	8	33
β-strand	59-61	3	33
α-helix	66-68	3
β-strand	69-70	2	31
β-strand	73	1	31
β-strand	79-84	6	31
α-helix	89-91	3
β-strand	93-100	8	33
β-strand	115-118	4	33
β-strand	122-124	3	33
β-strand	125-126	2	32
α-helix	132-134	3
β-strand	135-139	5	34
β-strand	152-160	9	34
β-strand	165-169	5	35
α-helix	170-172	3
β-strand	179-180	2	34
α-helix	181-183	3
β-strand	191-198	8	34
α-helix	201-203	3
β-strand	211-215	5	35
β-strand	220-222	3	35

Chain G: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	36
β-strand	12-13	2	37
β-strand	19-26	8	36
α-helix	30-32	3
β-strand	35-40	6	38
β-strand	47-52	6	38
β-strand	59-61	3	38
β-strand	66	1	36
β-strand	69-74	6	36
β-strand	79-84	6	36
α-helix	89-91	3
β-strand	93-100	8	38
β-strand	109-112	4	38
β-strand	117-118	2	38
β-strand	119-120	2	37
β-strand	126	1	39
β-strand	129-133	5	40
β-strand	144-154	11	40
β-strand	155	1	39
β-strand	160-163	4	41
α-helix	164-166	3
β-strand	172-174	3	40
α-helix	175-177	3
β-strand	178-179	2	40
β-strand	185-194	10	40
β-strand	203-209	7	41
β-strand	214-220	7	41

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	42
β-strand	12-15	4	43
β-strand	21-27	7	42
β-strand	35-40	6	43
β-strand	47-51	5	43
β-strand	55-56	2	43
α-helix	57	1
β-strand	64-68	5	42
β-strand	72-77	6	42
α-helix	82-84	3
β-strand	87-92	6	43
β-strand	104-108	5	43
β-strand	113	1	44
α-helix	114-115	2
β-strand	116-120	5	45
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	45
β-strand	142	1	44
β-strand	147-152	6	46
β-strand	155-156	2	46
β-strand	161-162	2	45
β-strand	165	1	45
β-strand	175-184	10	45
α-helix	185-190	6
β-strand	193-199	7	46
β-strand	207-212	6	46

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Y10 Light Chain	A, H	protein	214	Homo sapiens
Y10 Heavy Chain	B, G	protein	264	Homo sapiens
D4-10 Light Chain	C, E	protein	214	Homo sapiens
D4-10 Heavy Chain	D, F	protein	270	Homo sapiens
Iron-regulated surface determinant protein B	I, J	protein	157	Staphylococcus aureus (strain MSSA476)	Q69YH5 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5D1Z_1 Y10 Light Chain (chains A, H)
DIQMTQSPSFLSASVGDRVTITCRASQGITTYLGWYQQRPGKAPQLLIYAASSLQSGVPP
RFSGSGSGTEFTLTISSLQPEDFATYYCQQLNTYPYTFGPGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, G), FASTA

>5D1Z_2 Y10 Heavy Chain (chains B, G)
AEVQLVESGGGVVQPGGSLRLSCAASGFTFNKFWMNWVRQAPGKGLEWVADIQVDGSEKN
YVDSVKGRFTISRDNGKNSLYLQMNSLRAEDTGVYYCARGRYDYWSGYLSPWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHHHHHHHH
GGDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 3 (C, E), FASTA

>5D1Z_3 D4-10 Light Chain (chains C, E)
DIQLTQSPSFLSASVADRVTITCRASQAVRSSLAWYQQKPGKAPQLLIYSASTLENGVSS
RFSGSGPGTEFTLTISSLQPEDVGTYYCQQLNTYPFTFGPGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D, F), FASTA

>5D1Z_4 D4-10 Heavy Chain (chains D, F)
QVQLQESGPGLVKPSETLSLICTVSGGSISSSSYYWGWIRQTPERNLEWIGIIYFSGTTY
YNPSLQSRVSMSLDRSTNRFSLRLSSVTAADTAIYYCAKPKSRDRGGPGDDYFGMDVWGQ
GIMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCGGGSGHHHH
HHHHHHGGDYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 5 (I, J), FASTA

>5D1Z_5 Iron-regulated surface determinant protein B (chains I, J)
GPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVK
PARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTK
AVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT

Primary citation

Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Yeung, Y.A., Foletti, D., Deng, X. et al. Nat Commun (2016) 7:13376-13376. DOI 10.1038/ncomms13376 · PubMed

Other PDB entries of the same protein (UniProt Q69YH5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5INB 1.3 Å, RepoMan-PP1g (protein phosphatase 1, gamma isoform) holoenzyme complex
5IOH 2.57 Å, RepoMan-PP1a (protein phosphatase 1, alpha isoform) holoenzyme complex
5SW9 2.85 Å, The structure of the PP2A B56 subunit RepoMan complex

Browse structure collections

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