4BKF: Human EphA4 ectodomain

crystal structure of the human EphA4 ectodomain in complex with human ephrinB3. Determined by X-ray diffraction at 4.65 Å resolution. Released 3 Jul 2013.

Method: X-ray diffraction
Resolution: 4.65 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 10,126
Mol. weight: 166.17 kDa
Released: 3 Jul 2013

Explore 4BKF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BKF contains 53 α-helices and 121 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: 22 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	1
α-helix	36-38	3
β-strand	46-48	3	2
β-strand	55-60	6	1
β-strand	66-73	8	1
β-strand	82-85	4	2
α-helix	86-88	3
β-strand	89-90	2	2
β-strand	97-105	9	1
β-strand	106	1	3
α-helix	108-110	3
α-helix	117-119	3
β-strand	121-129	9	2
α-helix	139-141	3
β-strand	143-149	7	2
β-strand	154	1	3
β-strand	158	1	4
α-helix	162-163	2
β-strand	167-173	7	1
β-strand	180-187	8	2
β-strand	191-202	12	1
β-strand	203-204	2	5
β-strand	208-209	2	6
β-strand	212-213	2	6
β-strand	217-218	2	5
α-helix	219-220	2
β-strand	227-229	3	7
α-helix	231-232	2
β-strand	233	1	6
α-helix	234	1
β-strand	237	1	8
β-strand	244	1	9
β-strand	245-247	3	7
β-strand	253	1	7
β-strand	257	1	9
α-helix	261	1
β-strand	262	1	8
α-helix	263	1
β-strand	266-267	2	10
β-strand	274-275	2	10
α-helix	276-277	2
β-strand	280-281	2	11
α-helix	289-290	2
β-strand	291-292	2	11
α-helix	293-294	2
α-helix	298-301	4
β-strand	304	1	11
α-helix	308-310	3
β-strand	314	1	12
α-helix	324-325	2
β-strand	326	1	12
α-helix	327-329	3
β-strand	335-339	5	13
β-strand	344-348	5	13
β-strand	360-366	7	14
β-strand	385	1	15
β-strand	393	1	14
β-strand	397-400	4	13
β-strand	401	1	15
α-helix	403-404	2
β-strand	408-417	10	14
α-helix	424-426	3
β-strand	431-435	5	14
β-strand	447-452	6	16
β-strand	457-461	5	16
α-helix	462-464	3
β-strand	471-480	10	17
α-helix	486-488	3
β-strand	489-493	5	17
β-strand	497-499	3	16
β-strand	509-517	9	17
β-strand	521	1	17
β-strand	528-530	3	17

Chain B: 21 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	18
α-helix	36-38	3
β-strand	46-48	3	19
β-strand	55-60	6	18
β-strand	66-73	8	18
β-strand	82-85	4	19
α-helix	86-88	3
β-strand	89-90	2	19
β-strand	97-105	9	18
β-strand	106	1	20
α-helix	108-110	3
α-helix	117-119	3
β-strand	121-129	9	19
α-helix	139-141	3
β-strand	143-149	7	19
β-strand	154	1	20
β-strand	158	1	21
α-helix	162-163	2
β-strand	167-173	7	18
β-strand	180-187	8	19
β-strand	191-202	12	18
β-strand	203-204	2	22
β-strand	208-209	2	23
β-strand	212-213	2	23
β-strand	217-218	2	22
α-helix	219-220	2
β-strand	227-229	3	24
α-helix	231-232	2
β-strand	233	1	23
α-helix	234	1
β-strand	237	1	25
β-strand	244	1	26
β-strand	245-247	3	24
β-strand	253	1	24
β-strand	257	1	26
α-helix	261	1
β-strand	262	1	25
α-helix	263	1
β-strand	266-267	2	27
β-strand	274-275	2	27
α-helix	276-277	2
β-strand	280-281	2	28
α-helix	289-290	2
β-strand	291-292	2	28
α-helix	293-294	2
α-helix	298-301	4
β-strand	304	1	28
α-helix	308-310	3
α-helix	324-325	2
β-strand	335-339	5	29
β-strand	344-348	5	29
β-strand	360-366	7	30
β-strand	385	1	31
β-strand	393	1	30
β-strand	397-400	4	29
β-strand	401	1	31
α-helix	403-404	2
β-strand	408-417	10	30
α-helix	424-426	3
β-strand	431-435	5	30
β-strand	447-452	6	32
β-strand	457-461	5	32
α-helix	462-464	3
β-strand	471-480	10	33
α-helix	486-488	3
β-strand	489-493	5	33
β-strand	497-499	3	32
β-strand	509-517	9	33
β-strand	528-530	3	33

Chains C and D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
β-strand	33-34	2	34
β-strand	49-50	2	35
α-helix	52-53	2
β-strand	57-62	6	34
β-strand	80-84	5	35
α-helix	87-90	4
β-strand	93	1	36
α-helix	94-95	2
β-strand	99-103	5	35
β-strand	111-116	6	34
β-strand	125	1	21
β-strand	134-139	6	35
β-strand	152	1	36
α-helix	155-158	4
β-strand	162-166	5	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-a receptor 4	A, B	protein	568	HOMO SAPIENS	P54764 (AlphaFold model)
Ephrin-B3	C, D	protein	183	HOMO SAPIENS	Q15768 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4BKF_1 EPHRIN TYPE-A RECEPTOR 4 (chains A, B)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGVTGSRVYPTNEVTLLDSRSVQGELGWIAS
PLEGGWEEVSIMDEKNTPIRTYQVCNVMEPSQNNWLRTDWITREGAQRVYIEIKFTLRDC
NSLPGVMGTCKETFNLYYYESDNDKERFIRENQFVKIDTIAADESFTQVDIGDRIMKLNT
EIRDVGPLSKKGFYLAFQDVGACIALVSVRVFYKKCPLTVRNLAQFPDTITGADTSSLVE
VRGSCVNNSEEKDVPKMYCGADGEWLVPIGNCLCNAGHEERSGECQACKIGYYKALSTDA
TCAKCPPHSYSVWEGATSCTCDRGFFRADNDAASMPCTRPPSAPLNLISNVNETSVNLEW
SSPQNTGGRQDISYNVVCKKCGAGDPSKCRPCGSGVHYTPQQNGLKTTKVSITDLLAHTN
YTFEIWAVNGVSKYNPNPDQSVSVTVTTNQAAPSSIALVQAKEVTRYSVALAWLEPDRPN
GVILEYEVKYYEKDQNERSYRIVRTAARNTDIKGLNPLTSYVFHVRARTAAGYGDFSEPL
EVTTNTVPSRIIGDGANSTGTKHHHHHH

Sequence of entity 2 (C, D), FASTA

>4BKF_2 EPHRIN-B3 (chains C, D)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGGLSLEPVYWNSANKRFQAEGGYVLYPQIG
DRLDLLCPRARPPGPHSSPSYEFYKLYLVEGAQGRRCEAPPAPNLLLTCDRPDLDLRFTI
KFQEYSPNLWGHEFRSHHDYYIIATSDGTREGLESLQGGVCLTRGMKVLLRVGQGTKHHH
HHH

Primary citation

Structurally Encoded Intraclass Differences in Epha Clusters Drive Distinct Cell Responses. Seiradake, E., Schaupp, A., Del Toro Ruiz, D. et al. Nat Struct Mol Biol (2013) 20:958. DOI 10.1038/NSMB.2617 · PubMed

Other PDB entries of the same protein (UniProt P54764 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OFV 1.43 Å, NMR-guided design of potent and selective EphA4 agonistic ligands
5JR2 1.75 Å, Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor
2WO1 1.85 Å, Crystal Structure of the EphA4 Ligand Binding Domain
4M4P 2.08 Å, Crystal structure of EPHA4 ectodomain
2WO3 2.35 Å, Crystal Structure of the EphA4-ephrinA2 complex
4W4Z 2.41 Å, Structure of the EphA4 LBD in complex with peptide
4W50 2.42 Å, Structure of the EphA4 LBD in complex with peptide
2WO2 2.45 Å, Crystal Structure of the EphA4-ephrinB2 complex
3GXU 2.5 Å, Crystal structure of Eph receptor and ephrin complex
9CY8 2.5 Å, Constrained b-hairpins targeting the EphA4 ligand binding domain
3CKH 2.8 Å, Crystal structure of Eph A4 receptor
4M4R 3.13 Å, Epha4 ectodomain complex with ephrin a5

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