3NKV: Rab1b covalently modified with AMP at Y77

Crystal structure of Rab1b covalently modified with AMP at Y77. Determined by X-ray diffraction at 1.7 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,086
Mol. weight: 41.57 kDa
Ligands: AMP, BA, MG, GNP
Released: 4 Aug 2010

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

Secondary structure: helices and β-sheets

3NKV contains 14 α-helices and 12 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	1
α-helix	21-30	10
β-strand	43-52	10	1
β-strand	55-64	10	1
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	1
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	1
α-helix	133-143	11
β-strand	147-149	3	1
α-helix	158-171	14

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7-15	9	2
α-helix	21-30	10
β-strand	43-52	10	2
β-strand	55-64	10	2
α-helix	68-70	3
α-helix	71-75	5
β-strand	83-89	7	2
α-helix	93-97	5
α-helix	99-109	11
β-strand	115-121	7	2
α-helix	133-142	10
β-strand	147-150	4	2
α-helix	158-172	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-1B	A, B	protein	175	Homo sapiens	Q9H0U4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3NKV_1 Ras-related protein Rab-1B (chains A, B)
GHMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKL
QIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLV
GNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMG

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2
BA	Barium ion	Ba	2
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Primary citation

The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b. Muller, M.P., Peters, H., Blumer, J. et al. Science (2010) 329:946-949. DOI 10.1126/science.1192276 · PubMed

Other PDB entries of the same protein (UniProt Q9H0U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3JZA 1.8 Å, Crystal structure of human Rab1b in complex with the GEF domain of DrrA/SidM from…
8ALK 2.15 Å, Structure of the Legionella phosphocholine hydrolase Lem3 in complex with its substrate…
5SZH 2.3 Å, Structure of human Rab1b in complex with the bMERB domain of Mical-cL
5O74 2.5 Å, Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from…
4I1O 2.7 Å, Crystal structure of the Legionella pneumophila GAP domain of LepB in complex with Rab1b…
5SZK 2.8 Å, Structure of human N-terminally engineered Rab1b in complex with the bMERB domain of…
6SKU 3.2 Å, Legionella effector AnkX in complex with human Rab1b
4HLQ 3.3 Å, Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of…

Browse structure collections

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