3LZF: Fab 2D1

Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin. Determined by X-ray diffraction at 2.8 Å resolution. Released 7 Apr 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 4
Atoms: 7,207
Mol. weight: 106.18 kDa
Ligands: NAG
Released: 7 Apr 2010

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

Secondary structure: helices and β-sheets

3LZF contains 28 α-helices and 102 β-strands across 4 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: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	24-26	3	2
β-strand	34-36	3	2
β-strand	39-41	3	3
β-strand	43-44	2	4
β-strand	51-54	4	5
β-strand	56	1	5
α-helix	57-58	2
β-strand	59-60	2	6
β-strand	64	1	7
α-helix	66-71	6
α-helix	74-79	6
β-strand	83A	1	8
β-strand	87-89	3	6
β-strand	95	1	7
β-strand	102	1	9
α-helix	105-112	8
β-strand	115-122	8	8
β-strand	131	1	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151	1	12
β-strand	155	1	10
β-strand	157	1	13
β-strand	160	1	13
α-helix	162-163	2
β-strand	164-169	6	14
β-strand	176-177	2	8
β-strand	180-184	5	9
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	229-233	5	9
β-strand	236-237	2	8
β-strand	242-247	6	14
β-strand	251-252	2	9
β-strand	254	1	12
β-strand	256-262	7	8
β-strand	267-269	3	6
α-helix	273	1
β-strand	274-279	6	5
β-strand	281-283	3	15
β-strand	286-287	2	15
β-strand	294-295	2	4
β-strand	301	1	16
β-strand	302-303	2	15
β-strand	305	1	17
α-helix	306	1
β-strand	307-308	2	4
β-strand	315-317	3	3
β-strand	321	1	2

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	18
β-strand	10	1	18
β-strand	13	1	1
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-57	20
α-helix	60-61	2
β-strand	62	1	17
β-strand	65	1	16
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-152	7
α-helix	163-170	8

Chain H: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
β-strand	32-39	10	21
β-strand	46-52	7	21
β-strand	57-59	3	21
β-strand	67-72	6	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-98	11	21
α-helix	100B-100C	2
β-strand	100D	1	21
β-strand	103	1	21
β-strand	107-109	3	21
β-strand	110-111	2	20
α-helix	115-116	2
β-strand	117	1	22
β-strand	120-124	5	23
β-strand	138-147	10	23
β-strand	148	1	22
β-strand	153-157	4	24
α-helix	162-164	3
β-strand	171-173	3	23
α-helix	174-176	3
β-strand	177-178	2	23
β-strand	185-193	9	23
β-strand	198	1	25
β-strand	203	1	25
β-strand	207-212	6	24
α-helix	213-215	3
β-strand	217-222	6	24

Chain L: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	26
β-strand	5	1	27
β-strand	9-13	4	28
β-strand	19-24	6	27
β-strand	33-38	6	28
β-strand	45-48	4	28
β-strand	49	1	29
β-strand	53	1	29
α-helix	54-55	2
β-strand	62-67	6	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	85-92	8	28
β-strand	95C-98	4	28
β-strand	99	1	26
β-strand	102-106	5	28
α-helix	108-110	3
β-strand	111	1	30
α-helix	112-113	2
β-strand	114-118	5	31
α-helix	119-120	2
α-helix	122-126	5
β-strand	130-139	10	31
β-strand	140	1	30
β-strand	145-149	5	32
β-strand	154-155	2	32
β-strand	159-161	3	31
α-helix	162-164	3
β-strand	165-166	2	31
β-strand	173-181	9	31
α-helix	183-186	4
β-strand	192-198	7	32
β-strand	203-209	7	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin, HA1 Subunit	A	protein	331	Influenza A virus	Q9WFX3
Hemagglutinin, HA2 Subunit	B	protein	179	Influenza A virus	Q9WFX3
2D1 Fab, Heavy Chain	H	protein	230	Homo sapiens
2D1 Fab, Light Chain	L	protein	217	Homo sapiens

Sequence of entity 1 (A), FASTA

>3LZF_1 Hemagglutinin, HA1 Subunit (chains A)
ADPGDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCN
IAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEI
FPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVL
WGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEP
GDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIH
PVTIGECPKYVRSTKLRMATGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>3LZF_2 Hemagglutinin, HA2 Subunit (chains B)
GLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMN
TQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYE
KVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVSGR

Sequence of entity 3 (H), FASTA

>3LZF_3 2D1 Fab, Heavy Chain (chains H)
EVQLVESGPALVKPTQTLTLTCSFSGFSLSTSGMSVSWIRQPPGKALEWLALIDWDDDTY
YITYSSSLKTRLTISKDTSKSQVVLTMTNMDPVDTATYYCARTLRVSGDYVRDFDLWGRG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 4 (L), FASTA

>3LZF_4 2D1 Fab, Light Chain (chains L)
QPVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVSWYQQVPGTAPKLLIYGNNERPSGVP
DRFSGSKSATSASLAISGLQSEDEADYYCAAWDDSLNGFWVFGGGTKLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus. Xu, R., Ekiert, D.C., Krause, J.C. et al. Science (2010) 328:357-360. DOI 10.1126/science.1186430 · PubMed

Other PDB entries of the same protein (UniProt Q9WFX3), best resolution first:

4GXX 1.8 Å, Crystal structure of the "avianized" 1918 influenza virus hemagglutinin
5VMC 2.15 Å, Influenza hemagglutinin H1 mutant DH1 in complex with 6'SLN
3GBN 2.2 Å, Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus…
5VMF 2.35 Å, Influenza hemagglutinin H1 mutant DH1D in complex with 6'SLN
5VMG 2.45 Å, Influenza hemagglutinin H1 mutant DH1E in complex with 6'SLN
4JUG 2.7 Å, Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G
4EEF 2.7 Å, Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918…
4JUH 2.81 Å, Crystal structure of 1918 pandemic influenza virus hemagglutinin mutant D225G complexed…
1RUZ 2.9 Å, 1918 H1 Hemagglutinin
4PY8 2.91 Å, Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin
5VMJ 2.95 Å, Influenza hemagglutinin H1 mutant DH1E in complex with 3'SLN
1RD8 3.0 Å, Crystal Structure of the 1918 Human H1 Hemagglutinin Precursor (HA0)

Browse structure collections

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