9B7B: Humanized 44H10 Fab Version 22

Crystal structure of humanized 44H10 Fab Version 22 in complex with HLA-DR (HLA-DRA*01:01/HLA-DRB1*04:01). Determined by X-ray diffraction at 3.08 Å resolution. Released 7 Aug 2024.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,878
Mol. weight: 191.26 kDa
Ligands: NAG
Released: 7 Aug 2024

Explore 9B7B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B7B contains 50 α-helices and 157 β-strands across 8 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
α-helix	37-39	3
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	53	1	2
α-helix	56-76	21
α-helix	80-83	4
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-127	2	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	2
α-helix	8-12	5
β-strand	34-45	12	1
β-strand	50-59	10	1
β-strand	62-68	7	1
β-strand	73-76	4	1
α-helix	79-81	3
α-helix	82-88	7
α-helix	92-101	10
α-helix	102-106	5
α-helix	107-111	5
α-helix	114-118	5
β-strand	122	1	6
β-strand	125-130	6	7
β-strand	142-149	8	7
β-strand	150	1	6
β-strand	155-160	6	8
β-strand	163-164	2	8
β-strand	169-171	3	7
β-strand	175-176	2	7
β-strand	182-188	7	7
β-strand	198-203	6	8
β-strand	211-214	4	8

Chain C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
β-strand	32-39	8	11
β-strand	46-51	6	11
β-strand	57-59	3	11
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	84-86	3
β-strand	88-96	9	11
β-strand	100D-101	2	11
β-strand	107-109	3	11
β-strand	110-111	2	10
α-helix	115-116	2
β-strand	117	1	12
α-helix	118-119	2
β-strand	120-124	5	13
β-strand	131	1	13
β-strand	133	1	14
β-strand	136-145	10	13
β-strand	146	1	12
β-strand	151-154	4	15
α-helix	155-157	3
β-strand	163-165	3	13
α-helix	166-168	3
β-strand	169-170	2	13
β-strand	176-184	9	13
α-helix	186-188	3
β-strand	194-200	7	15
β-strand	205-211	7	15

Chain D: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-13	4	17
β-strand	19-25	7	16
β-strand	33-38	6	17
β-strand	44-49	6	17
β-strand	53-54	2	17
α-helix	55	1
β-strand	62-67	6	16
β-strand	70-75	6	16
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	98	1	17
β-strand	102-106	5	17
β-strand	111	1	18
α-helix	112-114	3
β-strand	115-118	4	19
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	145-150	6	20
β-strand	153-154	2	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-186	4
β-strand	191-197	7	20
β-strand	205-210	6	20

Chain E: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	21
β-strand	19-26	8	21
β-strand	29-35	7	21
β-strand	40-43	4	21
α-helix	46-50	5
β-strand	53	1	22
α-helix	56-76	21
α-helix	80-83	4
β-strand	85	1	23
α-helix	86-87	2
β-strand	88-93	6	24
β-strand	103-112	10	24
β-strand	113	1	23
β-strand	118-123	6	25
β-strand	126-127	2	25
β-strand	133-134	2	24
β-strand	138-139	2	24
β-strand	145-153	9	24
β-strand	160-166	7	25
β-strand	174-179	6	25

Chain F: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	22
α-helix	8-12	5
β-strand	34-45	12	21
β-strand	50-59	10	21
β-strand	62-68	7	21
β-strand	73-76	4	21
α-helix	79-81	3
α-helix	82-88	7
α-helix	92-101	10
α-helix	102-106	5
α-helix	107-111	5
α-helix	114-118	5
β-strand	122	1	26
β-strand	125-130	6	27
β-strand	142-149	8	27
β-strand	150	1	26
β-strand	155-160	6	28
β-strand	163-165	3	28
β-strand	169-171	3	27
β-strand	175-176	2	27
β-strand	182-188	7	27
β-strand	198-203	6	28
β-strand	211-215	5	28

Chain G: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	29
β-strand	11-12	2	30
β-strand	17-25	9	29
β-strand	32-39	8	31
β-strand	46-51	6	31
β-strand	57-59	3	31
β-strand	67-72	6	29
β-strand	77-82A	7	29
α-helix	84-86	3
β-strand	88-96	9	31
α-helix	100C	1
β-strand	100D-103	4	31
β-strand	107-109	3	31
β-strand	110-111	2	30
α-helix	115-116	2
β-strand	117	1	32
α-helix	118-119	2
β-strand	120-124	5	33
β-strand	131	1	33
β-strand	133	1	14
β-strand	136-145	10	33
β-strand	146	1	32
β-strand	150-154	5	34
β-strand	159	1	34
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-184	9	33
β-strand	194-200	7	34
β-strand	205-211	7	34

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-14	5	36
β-strand	19-25	7	35
β-strand	33-38	6	36
β-strand	44-49	6	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	56	1	37
β-strand	58	1	37
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	84-90	7	36
α-helix	96	1
β-strand	98	1	36
β-strand	102-107	6	36
β-strand	111	1	38
α-helix	112-113	2
β-strand	114-118	5	39
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	39
β-strand	140	1	38
β-strand	145-150	6	40
β-strand	153-154	2	40
β-strand	159-163	5	39
α-helix	164-167	4
β-strand	173-182	10	39
α-helix	183-187	5
β-strand	191-197	7	40
β-strand	205-210	6	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, E	protein	190	Homo sapiens	P01903 (AlphaFold model)
Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain	B, F	protein	226	Homo sapiens	A0A1V1IGJ9 (AlphaFold model)
h44H10-V22 Antibody, heavy chain	C, G	protein	223	Homo sapiens
h44H10-V22 Antibody, light chain	D, H	protein	214	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>9B7B_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, E)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGENLYFQ

Sequence of entity 2 (B, F), FASTA

>9B7B_2 Hemagglutinin HA1 chain, HLA class II histocompatibility antigen DR beta chain (chains B, F)
GAPKYVKQNTLKLATSGGSGSIEGRGSGDTRPRFLEQVKHECHFFNGTERVRFLDRYFYH
QEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQR
RVYPEVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDW
TFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRATGGENLYFQ

Sequence of entity 3 (C, G), FASTA

>9B7B_3 h44H10-V22 Antibody, heavy chain (chains C, G)
QVQLQESGPGLVKPSETLSLTCTVSGFSLTSYGVHWIRQPPGKGLEWIGVIWAGGSINYN
SALMSRVTISKDTSKNQVSLKLSSVTAADTAVYYCARAYGDYVHYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 4 (D, H), FASTA

>9B7B_4 h44H10-V22 Antibody, light chain (chains D, H)
DIQMTQSPSSLSASVGDRVTITCRASQEISGYLTWLQQKPGKAPKLLIYAASTLDSGVPK
RFSGSRSGTDFTLTISSLQPEDFATYYCLQYTNYPLTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (SO4) are not listed.

Primary citation

Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework. Kassardjian, A., Ivanochko, D., Barber, B. et al. Antibodies (Basel) (2024) 13. DOI 10.3390/antib13030057 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

Browse structure collections

About this viewer

MolViewer shows 9B7B directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.