5VMG: Influenza hemagglutinin H1 mutant DH1E

Influenza hemagglutinin H1 mutant DH1E in complex with 6'SLN. Determined by X-ray diffraction at 2.45 Å resolution. Released 8 Nov 2017.

Method: X-ray diffraction
Resolution: 2.45 Å
Organisms: Influenza A virus (A/New_York/1/18(H1N1)), Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Chains: 6
Atoms: 12,355
Mol. weight: 176.33 kDa
Ligands: NAG
Released: 8 Nov 2017

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

Secondary structure: helices and β-sheets

5VMG contains 41 α-helices and 152 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: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	8	1	2
β-strand	15-16	2	3
β-strand	24-25	2	3
β-strand	26	1	4
β-strand	29-31	3	5
β-strand	33-34	2	6
β-strand	41-44	4	7
β-strand	47	1	7
α-helix	48-49	2
β-strand	50-51	2	8
β-strand	55	1	9
α-helix	57-62	6
α-helix	65-67	3
β-strand	76	1	10
β-strand	79-81	3	8
β-strand	87	1	9
β-strand	95	1	10
α-helix	98-104	7
β-strand	108-115	8	10
α-helix	119-122	4
β-strand	127	1	11
β-strand	132-137	6	12
β-strand	140-142	3	12
β-strand	147-149	3	10
β-strand	151	1	11
β-strand	153	1	13
β-strand	156	1	13
α-helix	158-159	2
β-strand	160-165	6	14
β-strand	171-180	10	10
α-helix	184-191	8
β-strand	198-201	4	14
β-strand	206-209	4	14
β-strand	219	1	15
β-strand	222	1	15
β-strand	225-233	9	10
α-helix	234	1
β-strand	238-243	6	14
β-strand	247-250	4	10
β-strand	252-258	7	10
β-strand	264-266	3	8
α-helix	270	1
β-strand	271-276	6	7
β-strand	278-279	2	16
β-strand	284-285	2	16
β-strand	291-292	2	6
β-strand	299-300	2	16
α-helix	303	1
β-strand	304-305	2	6
β-strand	312-314	3	5
β-strand	318	1	4

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	17
β-strand	10	1	17
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-57	20
β-strand	64-65	2	16
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-134	5	1
β-strand	137-140	4	1
α-helix	146-153	8

Chain C: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	8	1	19
β-strand	15-16	2	20
β-strand	24-25	2	20
β-strand	26	1	21
β-strand	29-31	3	22
β-strand	33-34	2	23
β-strand	41-44	4	24
β-strand	47	1	24
α-helix	48-49	2
β-strand	50-51	2	25
β-strand	55	1	26
α-helix	57-62	6
α-helix	65-67	3
β-strand	76	1	27
β-strand	79-81	3	25
β-strand	87	1	26
β-strand	95	1	27
α-helix	98-104	7
β-strand	108-115	8	27
α-helix	119-122	4
β-strand	127	1	28
β-strand	132-137	6	29
β-strand	140-142	3	29
β-strand	147-149	3	27
β-strand	151	1	28
β-strand	153	1	30
β-strand	156	1	30
α-helix	158-159	2
β-strand	160-165	6	31
β-strand	171-180	10	27
α-helix	184-191	8
β-strand	198-201	4	31
β-strand	206-209	4	31
β-strand	219	1	32
β-strand	222	1	32
β-strand	225-233	9	27
α-helix	234	1
β-strand	238-243	6	31
β-strand	247-250	4	27
β-strand	252-258	7	27
β-strand	264-266	3	25
α-helix	270	1
β-strand	271-276	6	24
β-strand	278-280	3	33
β-strand	283-285	3	33
β-strand	291-292	2	23
β-strand	299-300	2	33
α-helix	303	1
β-strand	304-305	2	23
β-strand	312-314	3	22
β-strand	318	1	21

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	34
β-strand	10	1	34
β-strand	14	1	19
β-strand	22-28	7	18
β-strand	31-36	6	18
α-helix	38-57	20
β-strand	64-65	2	33
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-134	5	18
β-strand	137-140	4	18
α-helix	146-154	9

Chain E: 9 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	35
β-strand	8	1	36
β-strand	15-16	2	37
β-strand	24-25	2	37
β-strand	26	1	38
β-strand	29-31	3	39
β-strand	33-34	2	40
β-strand	41-44	4	41
β-strand	47	1	41
α-helix	48-49	2
β-strand	50-51	2	42
β-strand	55	1	43
α-helix	57-62	6
α-helix	65-67	3
β-strand	76	1	44
β-strand	79-81	3	42
β-strand	87	1	43
β-strand	95	1	45
α-helix	98-104	7
β-strand	108	1	44
β-strand	112-115	4	45
α-helix	119-122	4
β-strand	126-127	2	46
β-strand	132-137	6	47
β-strand	140-142	3	47
β-strand	147-149	3	45
β-strand	151-152	2	46
β-strand	153	1	48
β-strand	156	1	48
β-strand	160-165	6	49
β-strand	171-180	10	45
α-helix	184-191	8
β-strand	198-201	4	49
β-strand	206-209	4	49
β-strand	219	1	50
β-strand	222	1	50
β-strand	225-233	9	45
α-helix	234	1
β-strand	238-243	6	49
β-strand	247-250	4	45
β-strand	252-256	5	45
β-strand	258	1	44
β-strand	264-266	3	42
α-helix	270	1
β-strand	271-276	6	41
β-strand	278-279	2	51
β-strand	284	1	51
β-strand	291-292	2	40
β-strand	299-300	2	51
α-helix	303	1
β-strand	304-305	2	40
β-strand	312-314	3	39
β-strand	318	1	38

Chain F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	52
β-strand	10	1	52
β-strand	14	1	36
β-strand	22-28	7	35
β-strand	31-36	6	35
α-helix	38-57	20
β-strand	64-65	2	51
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	35
β-strand	137-140	4	35
α-helix	146-154	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A, C, E	protein	326	Influenza A virus (A/New_York/1/18(H1N1))	Q9WFX4
Hemagglutinin HA2	B, D, F	protein	191	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)	Q9WFX3

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

>5VMG_1 Hemagglutinin HA1 (chains A, C, E)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGW
LLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKT
SSWPNHETTGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHH
PPTGTEQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRGLASRMNYYWTLLEPGDTIT
FEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIG
ECPKYVRSTKLRMATGLRNIPSIQSR

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

>5VMG_2 Hemagglutinin HA2 (chains B, D, F)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVKLES
MGVYQGALVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Determinant of receptor-preference switch in influenza hemagglutinin. Ni, F., Kondrashkina, E., Wang, Q. Virology (2017) 513:98-107. DOI 10.1016/j.virol.2017.10.010 · PubMed

Other PDB entries of the same protein (UniProt Q9WFX4), best resolution first:

5VMJ 2.95 Å, Influenza hemagglutinin H1 mutant DH1E in complex with 3'SLN

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