3MX0: EphA2 ectodomain

Crystal Structure of EphA2 ectodomain in complex with ephrin-A5. Determined by X-ray diffraction at 3.51 Å resolution. Released 30 Jun 2010.

Method: X-ray diffraction
Resolution: 3.51 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,574
Mol. weight: 124.33 kDa
Ligands: NAG
Released: 30 Jun 2010

Explore 3MX0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MX0 contains 15 α-helices and 123 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, 52 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	1
β-strand	44-45	2	2
β-strand	53-55	3	3
β-strand	58-59	2	4
β-strand	62-63	2	4
β-strand	66-68	3	3
β-strand	79-82	4	2
β-strand	86-87	2	5
β-strand	94-96	3	1
β-strand	99-101	3	3
β-strand	102-103	2	6
β-strand	120-121	2	2
β-strand	122-123	2	7
β-strand	124-126	3	5
β-strand	140-141	2	7
β-strand	150-151	2	6
α-helix	154-157	4
β-strand	163-165	3	3
β-strand	168-170	3	1
β-strand	177-179	3	5
β-strand	182-184	3	2
β-strand	190-193	4	3
β-strand	195-199	5	1
β-strand	200-201	2	8
α-helix	202-203	2
β-strand	204-205	2	9
β-strand	209-211	3	9
β-strand	214-215	2	8
β-strand	224-227	4	10
β-strand	229-230	2	9
β-strand	235	1	11
β-strand	244-247	4	10
β-strand	253	1	10
β-strand	257	1	10
β-strand	261	1	11
β-strand	266-267	2	12
β-strand	274-275	2	12
α-helix	276	1
β-strand	278	1	13
β-strand	280-281	2	14
β-strand	291-292	2	14
β-strand	297	1	15
β-strand	302	1	13
β-strand	304	1	14
α-helix	307-308	2
β-strand	309	1	15
α-helix	310	1
β-strand	314	1	16
β-strand	326	1	16
α-helix	328-331	4
β-strand	335-338	4	17
β-strand	344-348	5	17
β-strand	361-366	6	18
β-strand	384	1	19
β-strand	396-399	4	17
β-strand	400	1	19
β-strand	408-415	8	18
β-strand	427-432	6	18

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	20
β-strand	49-52	4	21
β-strand	57-61	5	20
β-strand	79-82	4	21
α-helix	84-88	5
β-strand	97-98	2	21
β-strand	113-117	5	20
β-strand	132	1	22
β-strand	134	1	22
β-strand	135-140	6	21
β-strand	148	1	23
β-strand	150	1	23
β-strand	153-158	6	21

Chain C: 7 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	29-30	2	24
α-helix	34-37	4
β-strand	44-46	3	25
β-strand	53-59	7	26
β-strand	62-70	9	26
β-strand	79-82	4	25
β-strand	86-87	2	25
β-strand	94-100	7	24
β-strand	102	1	26
β-strand	103	1	27
β-strand	119-126	8	25
β-strand	140-145	6	25
β-strand	151	1	27
α-helix	153-156	4
β-strand	164-170	7	24
β-strand	177-181	5	25
β-strand	184	1	25
β-strand	188-191	4	26
β-strand	193	1	24
β-strand	196-198	3	24
β-strand	200	1	28
α-helix	201-203	3
β-strand	204-205	2	29
β-strand	209-211	3	29
β-strand	215	1	28
β-strand	224-227	4	30
α-helix	228	1
β-strand	229-230	2	29
β-strand	235	1	31
β-strand	244-247	4	30
β-strand	253	1	30
β-strand	257	1	30
β-strand	261	1	31
β-strand	266-269	4	32
β-strand	272-275	4	32
β-strand	280-281	2	33
β-strand	291-292	2	33
α-helix	293	1
β-strand	297-298	2	34
β-strand	308-309	2	34
α-helix	310	1
α-helix	328-331	4
β-strand	337-338	2	35
β-strand	344-346	3	35
β-strand	362-366	5	36
β-strand	368	1	37
β-strand	377	1	37
β-strand	384-385	2	35
β-strand	392	1	36
β-strand	397-400	4	35
β-strand	408-414	7	36
β-strand	427-432	6	36

Chain D: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	38
β-strand	49-52	4	39
β-strand	57-59	3	38
β-strand	61	1	40
β-strand	77	1	41
β-strand	79-82	4	39
α-helix	84-88	5
β-strand	96-98	3	39
β-strand	102	1	41
β-strand	113	1	40
β-strand	116-117	2	38
β-strand	135-140	6	39
β-strand	148	1	42
β-strand	150	1	42
β-strand	153-158	6	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-A receptor 2	A, C	protein	409	Homo sapiens	P29317 (AlphaFold model)
Ephrin-A5	B, D	protein	138	Homo sapiens	P52803 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3MX0_1 Ephrin type-A receptor 2 (chains A, C)
KEVVLLDFAAAGGELGWLTHPYGKGWDLMQNIMNDMPIYMYSVCNVMSGDQDNWLRTNWV
YRGEAERIFIELKFTVRDCNSFPGGASSCKETFNLYYAESDLDYGTNFQKRLFTKIDTIA
PDEITVSSDFEARHVKLNVEERSVGPLTRKGFYLAFQDIGACVALLSVRVYYKKCPELLQ
GLAHFPETIAGSDAPSLATVAGTCVDHAVVPPGGEEPRMHCAVDGEWLVPIGQCLCQAGY
EKVEDACQACSPGFFKFEASESPCLECPEHTLPSPEGATSCECEEGFFRAPQDPASMPCT
RPPSAPHYLTAVGMGAKVELRWTPPQDSGGREDIVYSVTCEQCWPESGECGPCEASVRYS
EPPHGLTRTSVTVSDLEPHMNYTFTVEARNGVSGLVTSRSFRTASVSIN

Sequence of entity 2 (B, D), FASTA

>3MX0_2 Ephrin-A5 (chains B, D)
VADRYAVYWNSSNPRFQRGDYHIDVCINDYLDVFCPHYEDSVPEDKTERYVLYMVNFDGY
SACDHTSKGFKRWECNRPHSPNGPLKFSEKFQLFTPFSLGFEFRPGREYFYISSAIPDNG
RRSCLKLKVFVRPTNSCM

Ligands and cofactors

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

Primary citation

Architecture of Eph receptor clusters. Himanen, J.P., Yermekbayeva, L., Janes, P.W. et al. Proc Natl Acad Sci U S A (2010) 107:10860-10865. DOI 10.1073/pnas.1004148107 · PubMed

Other PDB entries of the same protein (UniProt P29317 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q7D 0.98 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6Q7B 1.01 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6FNG 1.04 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with an isomer of…
6Q7G 1.05 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6Q7C 1.05 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6Q7E 1.06 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
5NKF 1.1 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 3b
5NKG 1.1 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 3d
8BOM 1.12 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 14
6HES 1.13 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6Q7F 1.2 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…
6HET 1.21 Å, Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with the NVP-BHG712…

Browse structure collections

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