5UG0: Human antibody H2897

Human antibody H2897 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006. Determined by X-ray diffraction at 3.4 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Influenza A virus (A/Solomon Islands/3/2006(H1N1)), Homo sapiens
Chains: 4
Atoms: 7,416
Mol. weight: 108.1 kDa
Ligands: NAG
Released: 31 May 2017

Explore 5UG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UG0 contains 18 α-helices and 98 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: 6 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	9-11	3	2
β-strand	12	1	3
β-strand	19-20	2	4
β-strand	28-29	2	4
β-strand	30	1	5
β-strand	33-35	3	6
β-strand	37-38	2	7
β-strand	45-48	4	8
β-strand	54-55	2	9
β-strand	59	1	10
α-helix	61-66	6
β-strand	79	1	11
β-strand	83-85	3	9
β-strand	91	1	10
β-strand	99	1	12
α-helix	102-110	9
β-strand	114	1	11
β-strand	117-118	2	12
α-helix	123-126	4
β-strand	131	1	13
β-strand	133	1	12
β-strand	136-142	7	14
β-strand	144-146	3	14
β-strand	151-153	3	12
β-strand	155	1	13
β-strand	157	1	15
β-strand	160	1	15
β-strand	164-169	6	16
β-strand	175-184	10	12
α-helix	188-194	7
β-strand	202-206	5	16
β-strand	209-213	5	16
β-strand	223	1	17
β-strand	226	1	17
β-strand	229-237	9	12
α-helix	238	1
β-strand	242-247	6	16
β-strand	251-254	4	12
β-strand	257-260	4	12
β-strand	268-270	3	9
α-helix	274	1
β-strand	275-280	6	8
β-strand	282-284	3	18
β-strand	287-289	3	18
β-strand	295-296	2	7
β-strand	303-304	2	18
β-strand	305-306	2	19
β-strand	309	1	7
β-strand	316-318	3	6
β-strand	322	1	5
β-strand	325	1	20

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	13	1	20
β-strand	14	1	3
β-strand	22-24	3	2
β-strand	27	1	1
β-strand	32	1	1
β-strand	35-36	2	2
α-helix	38-58	21
β-strand	62-63	2	19
α-helix	72-74	3
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-131	2	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-170	12

Chain C: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	12	1	22
β-strand	19-25	7	21
β-strand	34-37	4	23
β-strand	47-49	3	23
β-strand	55	1	23
β-strand	63-68	6	21
β-strand	71-76	6	21
β-strand	88-91	4	23
β-strand	107	1	22
β-strand	118-119	2	24
α-helix	121-123	3
α-helix	126-128	3
β-strand	132-134	3	25
β-strand	136-137	2	24
β-strand	138-141	4	26
β-strand	146-152	7	27
β-strand	175-177	3	26
β-strand	181-183	3	25
α-helix	185-188	4
β-strand	194-200	7	27
β-strand	208-211	4	27

Chain D: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	28
β-strand	11-12	2	29
β-strand	18-25	8	28
α-helix	29-31	3
β-strand	32-39	8	30
β-strand	45-51	7	30
β-strand	57-58	2	30
β-strand	67-72	6	28
β-strand	77-82	6	28
β-strand	91-100	10	30
β-strand	103	1	14
β-strand	114-117	4	30
β-strand	118	1	28
β-strand	121-123	3	30
β-strand	124-125	2	29
β-strand	131	1	31
β-strand	134-135	2	32
β-strand	152-159	8	32
β-strand	160	1	31
β-strand	164-168	5	33
β-strand	177-179	3	32
α-helix	180-182	3
β-strand	183-184	2	32
β-strand	190-196	7	32
α-helix	207-209	3
β-strand	210-214	5	33
β-strand	219-221	3	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A	protein	327	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7UPX0
Hemagglutinin HA2	B	protein	182	Influenza A virus (A/Solomon Islands/3/2006(H1N1))	A7UPX0
2897 light chain	C	protein	216	Homo sapiens	Q6PIL8 (AlphaFold model)
2897 heavy chain	D	protein	232	Homo sapiens	Q6N089 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5UG0_1 Hemagglutinin HA1 (chains A)
EDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAG
WILGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPK
ESSWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVH
HPPNIGDQRALYHTENAYVSVVSSHYSRKFTPEIAKRPKVRDREGRINYYWTLLEPGDTI
IFEANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTI
GECPKYVRSAKLRMVTGLRNIPSIQSR

Sequence of entity 2 (B), FASTA

>5UG0_2 Hemagglutinin HA2 (chains B)
GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMN
TQFTAVGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYE
KVKSQLKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKIDGVRSLV
PR

Sequence of entity 3 (C), FASTA

>5UG0_3 2897 light chain (chains C)
EIVLTQSPGTLSLSPGEKATLSCRASQSVSSYYLGWYQQKPGQAPRLLIYETSRRATGIP
DRFSGSGSGTDFTLTISGLEPEDFAVYYCQHYGVSPVITFGGGTKVEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D), FASTA

>5UG0_4 2897 heavy chain (chains D)
EVQLVESGGGLVQPGGSLRLSCAASGFTFNIYDMHWVRQAPGKGLEWVSSITTAGDTYYP
GSVKGRFTTSRENAKNSLYLQMNSLRAGDTGVYYCTRGVREVGATGDDPFYYGMYVWGQG
TTVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

CryoEM Structure of an Influenza Virus Receptor-Binding Site Antibody-Antigen Interface. Liu, Y., Pan, J., Jenni, S. et al. J Mol Biol (2017) 429:1829-1839. DOI 10.1016/j.jmb.2017.05.011 · PubMed

Other PDB entries of the same protein (UniProt A7UPX0), best resolution first:

5W0D 1.9 Å, Inferred precursor (UCA) of the human antibody lineage K03.12 in complex with influenza…
4HKX 2.5 Å, Influenza hemagglutinin in complex with CH67 Fab
4YJZ 2.72 Å, Human antibody H2526 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
4YK4 2.8 Å, Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006
9E6J 2.98 Å, DH726-1 Fab bound to hemagglutinin from influenza A/Solomon Islands/3/2006
6Q0O 3.0 Å, human antibody H2227 lineage 652 in complex with influenza hemagglutinin head domain of…
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin
5UJZ 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK0 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK1 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…
5UK2 4.8 Å, CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface…

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