4KDN: Hemagglutinin of ferret-transmissible H5N1 virus

Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with avian receptor analog LSTa. Determined by X-ray diffraction at 2.48 Å resolution. Released 24 Jul 2013.

Method: X-ray diffraction
Resolution: 2.48 Å
Organism: Influenza A virus
Chains: 6
Atoms: 12,269
Mol. weight: 172.41 kDa
Ligands: NAG, SIA
Released: 24 Jul 2013

Explore 4KDN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KDN contains 37 α-helices and 145 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: 6 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	12	1	2
β-strand	19-20	2	3
β-strand	28-29	2	3
β-strand	30	1	4
β-strand	33-35	3	5
β-strand	37-38	2	6
β-strand	45-48	4	7
β-strand	51	1	7
β-strand	54-55	2	8
β-strand	59	1	9
α-helix	61-65	5
β-strand	80	1	10
β-strand	83-85	3	8
β-strand	91	1	9
β-strand	97-99	3	11
α-helix	102-109	8
β-strand	112	1	10
β-strand	114-119	6	11
α-helix	123-125	3
β-strand	129-130	2	12
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	11
β-strand	155-156	2	12
β-strand	157	1	14
β-strand	160	1	14
α-helix	162-163	2
β-strand	164-169	6	15
β-strand	175-184	10	11
α-helix	188-194	7
β-strand	202-205	4	15
β-strand	210-213	4	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	256-261	6	11
β-strand	268-270	3	8
β-strand	275-280	6	7
β-strand	282-284	3	17
β-strand	287-288	2	17
β-strand	295-296	2	6
β-strand	303-304	2	17
α-helix	307	1
β-strand	308-309	2	6
β-strand	316-318	3	5
β-strand	322	1	4

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	339-343	5
β-strand	348	1	2
β-strand	356-362	7	1
β-strand	365-370	6	1
α-helix	372-391	20
β-strand	398-399	2	17
α-helix	409-460	52
α-helix	461-463	3
β-strand	464-466	3	1
β-strand	471-474	4	1
α-helix	480-488	9
α-helix	494-507	14

Chain C: 7 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	18
β-strand	12	1	19
β-strand	30	1	20
β-strand	33-35	3	21
β-strand	37-38	2	22
β-strand	45-48	4	23
β-strand	51	1	23
β-strand	54-55	2	24
β-strand	59	1	25
α-helix	61-65	5
β-strand	80	1	26
β-strand	83-85	3	24
β-strand	91	1	25
β-strand	97-99	3	27
α-helix	102-109	8
β-strand	112	1	26
β-strand	114-119	6	27
α-helix	123-125	3
β-strand	130	1	28
β-strand	136-140	5	29
β-strand	145-146	2	29
β-strand	151-153	3	27
β-strand	155	1	28
β-strand	157	1	30
β-strand	160	1	30
α-helix	162-163	2
β-strand	164-169	6	31
β-strand	175-184	10	27
α-helix	188-194	7
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	32
β-strand	226	1	32
β-strand	229-237	9	27
α-helix	238	1
β-strand	242-247	6	31
β-strand	251-254	4	27
β-strand	256-261	6	27
β-strand	268-270	3	24
β-strand	275-280	6	23
β-strand	282-284	3	33
β-strand	287-288	2	33
β-strand	295-296	2	22
β-strand	303-304	2	33
α-helix	307	1
β-strand	308-309	2	22
β-strand	316-318	3	21
β-strand	322	1	20

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	339-343	5
β-strand	348	1	19
β-strand	356-361	6	18
β-strand	366-370	5	18
α-helix	372-391	20
β-strand	398-399	2	33
α-helix	409-460	52
α-helix	461-463	3
β-strand	464-466	3	18
β-strand	471-474	4	18
α-helix	480-488	9
α-helix	494-507	14

Chain E: 6 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	34
β-strand	12	1	35
β-strand	19-20	2	36
β-strand	28-29	2	36
β-strand	30	1	37
β-strand	33-35	3	38
β-strand	37-38	2	39
β-strand	45-48	4	40
β-strand	51	1	40
β-strand	54-55	2	41
β-strand	59	1	42
α-helix	61-65	5
β-strand	80	1	43
β-strand	83-85	3	41
β-strand	91	1	42
β-strand	97-99	3	44
α-helix	102-109	8
β-strand	112	1	43
β-strand	114-119	6	44
α-helix	123-125	3
β-strand	130	1	45
β-strand	136-140	5	46
β-strand	145-146	2	46
β-strand	151-153	3	44
β-strand	155	1	45
β-strand	157	1	47
β-strand	160	1	47
α-helix	162-163	2
β-strand	164-169	6	48
β-strand	175-184	10	44
α-helix	188-194	7
β-strand	202-205	4	48
β-strand	210-213	4	48
β-strand	223	1	49
β-strand	226	1	49
β-strand	229-237	9	44
β-strand	242-247	6	48
β-strand	251-254	4	44
β-strand	256-261	6	44
β-strand	268-270	3	41
β-strand	275-280	6	40
β-strand	282-284	3	50
β-strand	287-288	2	50
β-strand	295-296	2	39
β-strand	303-304	2	50
α-helix	307	1
β-strand	308-309	2	39
β-strand	316-318	3	38
β-strand	322	1	37

Chain F: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	339-343	5
β-strand	348	1	35
β-strand	356-361	6	34
β-strand	366-370	5	34
α-helix	372-391	20
β-strand	398-399	2	50
α-helix	409-460	52
α-helix	461-463	3
β-strand	464-466	3	34
β-strand	471-474	4	34
α-helix	480-488	9
α-helix	494-505	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, C, E	protein	322	Influenza A virus	Q6DQ33
Hemagglutinin	B, D, F	protein	175	Influenza A virus	Q6DQ33

Sequence of entity 1 (A, C, E), FASTA

>4KDN_1 Hemagglutinin (chains A, C, E)
QDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKKHNGKLCDLDGVKPLILRDCSVAG
WLLGNPMCDEFINVPEWSYIVEKANPVNDLCYPGDFNDYEELKHLLSRINHFEKIQIIPK
SSWSSHEASLGVSSACPYQGKSSFFRNVVWLIKKDSTYPTIKRSYNNTNQEDLLVLWGIH
HPNDAAEQTKLYQNPTTYISVGTSTLNQRLVPRIATRSKVKGLSGRMEFFWTILKPNDAI
NFESNGNFIAPEYAYKIVKKGDSTIMKSELEYGNCNTKCQTPMGAINSSMPFHNIHPLTI
GECPKYVKSNRLVLAIGLRNSP

Sequence of entity 2 (B, D, F), FASTA

>4KDN_2 Hemagglutinin (chains B, D, F)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
SIA	N-acetyl-alpha-neuraminic acid	C11 H19 N O9	2

Primary citation

Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut). Lu, X., Shi, Y., Zhang, W. et al. Protein Cell (2013) 4:502-511. DOI 10.1007/s13238-013-3906-z · PubMed

Other PDB entries of the same protein (UniProt Q6DQ33), best resolution first:

4FQI 1.71 Å, Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin
4XNQ 2.0 Å, Antibody hemagglutinin Complexes
6CF5 2.04 Å, Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in…
4KDO 2.4 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex…
4KDM 2.5 Å, Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
4XNM 2.51 Å, Antibody Influenza H5 Complex
3GBM 2.7 Å, Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.
4XRC 2.74 Å, Antibody hemagglutinin Complexes
5A3I 2.89 Å, Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5…
6E3H 2.9 Å, Crystal structure of S9-3-37 bound to H5 influenza hemagglutinin
4N5Z 2.95 Å, Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D,…
6E7G 3.09 Å, Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1…

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