1JPN: GMPPNP Complex of SRP GTPase NG Domain

GMPPNP Complex of SRP GTPase NG Domain. Determined by X-ray diffraction at 1.9 Å resolution. Released 2 Feb 2002.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Thermus aquaticus
Chains: 2
Atoms: 5,117
Mol. weight: 66.31 kDa
Ligands: CA, GNP
Released: 2 Feb 2002

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

Secondary structure: helices and β-sheets

1JPN contains 28 α-helices and 16 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: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	24-40	17
α-helix	45-61	17
α-helix	70-85	16
α-helix	93-95	3
β-strand	99-104	6	2
α-helix	111-124	14
β-strand	129-133	5	2
α-helix	139-152	14
β-strand	156-158	3	2
α-helix	159-160	2
α-helix	165-178	14
β-strand	183-187	5	2
α-helix	196-209	14
β-strand	213-219	7	2
α-helix	220-222	3
α-helix	224-236	13
β-strand	241-245	5	2
α-helix	254-263	10
β-strand	267-271	5	2
β-strand	279-281	3	2
α-helix	284-291	8

Chain B: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	24-40	17
α-helix	45-60	16
α-helix	70-85	16
α-helix	93-95	3
β-strand	99-104	6	1
α-helix	111-123	13
β-strand	129-133	5	1
α-helix	139-151	13
β-strand	156-158	3	1
α-helix	159-160	2
α-helix	165-178	14
β-strand	183-187	5	1
α-helix	196-209	14
β-strand	213-219	7	1
α-helix	220-222	3
α-helix	225-236	12
β-strand	241-245	5	1
α-helix	254-263	10
β-strand	267-271	5	1
β-strand	279-281	3	1
α-helix	284-291	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle protein	A, B	protein	296	Thermus aquaticus	O07347 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1JPN_1 SIGNAL RECOGNITION PARTICLE PROTEIN (chains A, B)
MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEAL
GKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLAL
YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEA
RDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT
GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Water and common crystallization additives (ACY) are not listed.

Primary citation

The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase. Padmanabhan, S., Freymann, D.M. Structure (2001) 9:859-867. DOI 10.1016/S0969-2126(01)00641-4 · PubMed

Other PDB entries of the same protein (UniProt O07347 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LS1 1.1 Å, T. aquaticus Ffh NG Domain at 1.1A Resolution
2J45 1.14 Å, Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
2J46 1.14 Å, Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
2C04 1.15 Å, GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
2C03 1.24 Å, GDP complex of srp gtpase ffh ng domain
1RJ9 1.9 Å, Structure of the heterodimer of the conserved GTPase domains of the Signal Recognition…
2J7P 1.97 Å, GMPPNP-stabilized NG domain complex of the SRP GTPases Ffh and FtsY
2NG1 2.02 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1NG1 2.03 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1FFH 2.05 Å, N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus
1OKK 2.05 Å, Homo-heterodimeric complex of the srp gtpases
1O87 2.1 Å, A new MgGDP complex of the Ffh NG domain

Browse structure collections

About this viewer

MolViewer shows 1JPN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.