2JIX: Abt-007 FAB fragment

Crystal structure of ABT-007 FAB fragment with the soluble domain of EPO receptor. Determined by X-ray diffraction at 3.2 Å resolution. Released 10 Jul 2007.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: HOMO SAPIENS
Chains: 9
Atoms: 14,781
Mol. weight: 213.15 kDa
Released: 10 Jul 2007

Explore 2JIX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2JIX contains 58 α-helices and 200 β-strands across 9 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: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
β-strand	84-90	7	2
α-helix	96	1
β-strand	97	1	2
β-strand	99	1	1
β-strand	103-107	5	2
β-strand	111	1	3
β-strand	114-118	5	4
β-strand	129-130	2	5
β-strand	133-137	5	4
β-strand	139	1	6
β-strand	140	1	3
β-strand	146-150	5	7
β-strand	154	1	7
β-strand	159-163	5	4
β-strand	173	1	6
β-strand	175-179	5	4
β-strand	181-182	2	5
α-helix	183-188	6
β-strand	192-196	5	7
β-strand	205	1	7
β-strand	208	1	7

Chain B: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	27-30	4	8
β-strand	36-42	7	8
β-strand	53-58	6	9
β-strand	66	1	9
β-strand	70-73	4	8
β-strand	79-84	6	8
β-strand	96-102	7	9
β-strand	106-113	8	9
α-helix	115-117	3
β-strand	119-120	2	8
α-helix	121-124	4
β-strand	125-132	8	10
β-strand	137-143	7	10
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	11
α-helix	163-166	4
β-strand	171-174	4	11
α-helix	175	1
β-strand	180-183	4	10
α-helix	186-187	2
β-strand	191-200	10	11
β-strand	207-208	2	8
α-helix	209-214	6
β-strand	216-219	4	11

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	29-30	2	12
β-strand	36-41	6	12
α-helix	50-52	3
β-strand	54-58	5	13
β-strand	70-74	5	12
β-strand	78-84	7	12
β-strand	97-101	5	13
β-strand	107-112	6	13
α-helix	115-117	3
β-strand	119-120	2	12
α-helix	121-123	3
β-strand	125-131	7	14
β-strand	138-143	6	14
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-161	8	10
β-strand	170-174	5	10
α-helix	175	1
β-strand	180-183	4	14
α-helix	186-187	2
β-strand	191-200	10	10
β-strand	207-208	2	12
α-helix	209-214	6
β-strand	216-219	4	10

Chain D: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	46-52	7	17
β-strand	58-59	2	17
α-helix	61-64	4
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	87-89	3
β-strand	91-98	8	17
β-strand	105-106	2	17
β-strand	110-112	3	17
β-strand	113-114	2	16
α-helix	120-122	3
β-strand	123-124	2	18
α-helix	126	1
β-strand	127	1	18
α-helix	128-129	2
β-strand	141-148	8	18
β-strand	157	1	19
α-helix	158-160	3
β-strand	162	1	19
β-strand	168	1	18
α-helix	169-171	3
β-strand	172-173	2	18
β-strand	179-185	7	18
α-helix	190-192	3
β-strand	198-200	3	19
β-strand	203	1	20
α-helix	204-206	3
β-strand	208	1	20
β-strand	211-213	3	19

Chain E: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	27-29	3	21
β-strand	30	1	22
β-strand	37-42	6	21
β-strand	54-58	5	23
α-helix	62-64	3
β-strand	65-67	3	23
β-strand	70-73	4	21
β-strand	79-84	6	21
β-strand	96-101	6	23
β-strand	107-113	7	23
α-helix	115-117	3
β-strand	119	1	22
α-helix	121-124	4
β-strand	125-131	7	24
β-strand	138-143	6	24
α-helix	144-145	2
α-helix	151-153	3
β-strand	154-162	9	14
β-strand	170-174	5	14
β-strand	180-183	4	24
α-helix	186-187	2
β-strand	191-200	10	14
β-strand	207	1	22
α-helix	209-214	6
β-strand	216-219	4	14

Chain F: 1 helix, 30 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	25
β-strand	10-12	3	26
β-strand	18	1	27
β-strand	21-25	5	25
β-strand	33-39	7	26
β-strand	46-52	7	26
β-strand	57-59	3	26
β-strand	68-69	2	28
β-strand	72	1	25
β-strand	77-79	3	25
β-strand	80-81	2	28
β-strand	82	1	27
β-strand	91-96	6	26
β-strand	106	1	26
β-strand	110-114	5	26
β-strand	120	1	29
β-strand	123	1	30
β-strand	140	1	31
β-strand	146-148	3	30
β-strand	149	1	29
β-strand	154-155	2	32
β-strand	167-168	2	33
α-helix	169-171	3
β-strand	179-180	2	30
β-strand	183-184	2	33
β-strand	186	1	31
β-strand	197-198	2	34
β-strand	201-202	2	32
β-strand	203	1	35
β-strand	208	1	35
β-strand	213-214	2	34

Chain G: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-14	5	17
β-strand	19-25	7	36
β-strand	33-38	6	17
β-strand	45-49	5	17
β-strand	53-54	2	17
β-strand	62-67	6	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	84-90	7	17
α-helix	96	1
β-strand	97-98	2	17
β-strand	102-107	6	17
β-strand	111	1	37
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-137	8	38
β-strand	140	1	37
β-strand	144-150	7	39
β-strand	153-154	2	39
α-helix	155	1
β-strand	159	1	38
β-strand	163	1	38
β-strand	175-181	7	38
α-helix	185-188	4
β-strand	192-198	7	39
β-strand	205-209	5	39

Chain H: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	40
β-strand	11	1	41
β-strand	17-25	9	40
α-helix	29-31	3
β-strand	33-39	7	42
β-strand	46-52	7	42
β-strand	57-59	3	42
α-helix	64-66	3
β-strand	69-72	4	40
β-strand	77-83	7	40
β-strand	91-98	8	42
β-strand	103	1	42
β-strand	110-112	3	42
β-strand	113	1	41
β-strand	120	1	43
α-helix	121-122	2
β-strand	123-126	4	44
α-helix	131-133	3
β-strand	138	1	45
β-strand	141-148	8	44
β-strand	149	1	43
β-strand	154-157	4	46
β-strand	166-168	3	44
α-helix	169-171	3
β-strand	172-173	2	44
β-strand	179-185	7	44
β-strand	188	1	45
β-strand	198	1	47
β-strand	199-203	5	46
β-strand	208-210	3	46
β-strand	213	1	47

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Abt-007 FAB fragment	A, G, L	protein	214	HOMO SAPIENS	Q7Z3Y4 (AlphaFold model)
Erythropoietin receptor	B, C, E	protein	225	HOMO SAPIENS	P19235 (AlphaFold model)
Abt-007 FAB fragment	D, F, H	protein	217	HOMO SAPIENS	Q6GMX6 (AlphaFold model)

Sequence of entity 1 (A, G, L), FASTA

>2JIX_1 ABT-007 FAB FRAGMENT (chains A, G, L)
DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPKRLIYAASSLQSGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCLQHNTYPPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, C, E), FASTA

>2JIX_2 ERYTHROPOIETIN RECEPTOR (chains B, C, E)
APPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLE
DEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVL
LDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTE
CVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLD

Sequence of entity 3 (D, F, H), FASTA

>2JIX_3 ABT-007 FAB FRAGMENT (chains D, F, H)
QVQLQESGPGLVKPSETLSLTCTVSGASISSYYWSWIRQPPGKGLEWIGYIGGEGSTNYN
PSLKSRVTISVDTSKNQFSLKLRSVTAADTAVYYCARERLGIGDYWGQGTLVTVSSASTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Primary citation

A Potent Erythropoietin-Mimicking Human Antibody Interacts Through a Novel Binding Site. Liu, Z., Stoll, V.S., Devries, P. et al. Blood (2007) 110:2408. DOI 10.1182/BLOOD-2007-04-083998 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MY5 1.73 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
4PUB 1.75 Å, Crystal structure of Fab DX-2930
1L7I 1.8 Å, Crystal Structure of the anti-ErbB2 Fab2C4
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
4OGY 2.1 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom…
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
9MY8 2.3 Å, D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD
4OGX 2.4 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom…
8CWJ 2.45 Å, Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain…

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