2BBA: Ephrin type-B receptor 4

Crystal Structure and Thermodynamic Characterization of the EphB4 Receptor in Complex with an ephrin-B2 Antagonist Peptide Reveals the Determinants for Receptor Specificity. Determined by X-ray diffraction at 1.65 Å resolution. Released 18 Jul 2006.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,803
Mol. weight: 22.99 kDa
Released: 18 Jul 2006

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

Secondary structure: helices and β-sheets

2BBA contains 4 α-helices and 18 β-strands across 2 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, 18 β-strands

Element	Residues	Length	Sheet
β-strand	17-22	6	1
α-helix	23-25	3
β-strand	33-35	3	2
β-strand	43-48	6	1
β-strand	54-61	8	1
β-strand	70-74	5	2
α-helix	75-77	3
β-strand	78-79	2	2
β-strand	86-94	9	1
β-strand	95	1	3
α-helix	97-99	3
β-strand	110-118	9	2
β-strand	132	1	4
β-strand	135	1	4
β-strand	136-142	7	2
β-strand	147	1	3
β-strand	148	1	5
β-strand	156	1	5
β-strand	160-166	7	1
β-strand	173-181	9	2
β-strand	184-195	12	1

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	261-263	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ephrin type-B receptor 4	A	protein	185	Homo sapiens	P54760 (AlphaFold model)
Agonist peptide	P	protein	15

Sequence of entity 1 (A), FASTA

>2BBA_1 Ephrin type-B receptor 4 (chains A)
HHHHHEETLLNTKLETADLKWVTFPQVDGQWEELSGLDEEQHSVRTYEVCDVQRAPGQAH
WLRTGWVPRRGAVHVYATLRFTMLECLSLPRAGRSCKETFTVFYYESDADTATALTPAWM
ENPYIKVDTVAAEHLTRKRPGAEATGKVNVKTLRLGPLSKAGFYLAFQDQGACMALLSLH
LFYKK

Sequence of entity 2 (P), FASTA

>2BBA_2 Agonist peptide (chains P)
TNYLFSPNGPIARAW

Primary citation

Structure and thermodynamic characterization of the EphB4/Ephrin-B2 antagonist peptide complex reveals the determinants for receptor specificity. Chrencik, J.E., Brooun, A., Recht, M.I. et al. Structure (2006) 14:321-330. DOI 10.1016/j.str.2005.11.011 · PubMed

Other PDB entries of the same protein (UniProt P54760 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FNK 1.05 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with a…
6FNM 1.16 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with Dasatinib
6FNJ 1.24 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of…
6FNL 1.27 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase
6FNI 1.47 Å, Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712
2VWX 1.65 Å, ephB4 kinase domain inhibitor complex
2VWY 1.65 Å, ephB4 kinase domain inhibitor complex
2VWZ 1.65 Å, ephB4 kinase domain inhibitor complex
2VX1 1.65 Å, ephB4 kinase domain inhibitor complex
4BB4 1.65 Å, ephB4 kinase domain inhibitor complex
2XVD 1.7 Å, ephB4 kinase domain inhibitor complex
2X9F 1.75 Å, ephB4 kinase domain inhibitor complex

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