1TXU: Vps9 Domain of Rabex-5

Crystal Structure of the Vps9 Domain of Rabex-5. Determined by X-ray diffraction at 2.35 Å resolution. Released 21 Sept 2004.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,163
Mol. weight: 32.39 kDa
Ligands: MG
Released: 21 Sept 2004

Explore 1TXU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TXU contains 16 α-helices and 0 β-strands across 1 chain. 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: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	135-147	13
α-helix	150-169	20
α-helix	175-196	22
α-helix	204-223	20
α-helix	231-243	13
α-helix	262-277	16
α-helix	278-280	3
α-helix	284-306	23
α-helix	309-311	3
α-helix	312-314	3
α-helix	315-326	12
α-helix	331-341	11
α-helix	344-346	3
α-helix	351-367	17
α-helix	372-374	3
α-helix	378-386	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rab5 GDP/GTP exchange factor	A	protein	273	Homo sapiens	Q9UJ41 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1TXU_1 Rab5 GDP/GTP exchange factor (chains A)
MGHHHHHHGSSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSEC
AQDFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKR
IRALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNA
IKITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCC
AVAFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5. Delprato, A., Merithew, E., Lambright, D.G. Cell (2004) 118:607-617. DOI 10.1016/j.cell.2004.08.009 · PubMed

Other PDB entries of the same protein (UniProt Q9UJ41 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N3X 2.0 Å, Crystal structure of Rabex-5 CC domain
2C7N 2.1 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
2OT3 2.1 Å, Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
4N3Y 2.2 Å, Crystal structure of Rabex-5CC and Rabaptin-5C21 complex
2C7M 2.4 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
4N3Z 3.1 Å, Crystal structure of Rabex-5delta and Rabaptin-5C21 complex
4Q9U 4.62 Å, Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex

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