1O87: A new MgGDP complex of the Ffh NG domain

A new MgGDP complex of the Ffh NG domain. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Jan 2004.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: THERMUS AQUATICUS
Chains: 2
Atoms: 4,970
Mol. weight: 66.39 kDa
Ligands: MG, GDP
Released: 2 Jan 2004

Explore 1O87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1O87 contains 27 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: 13 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
β-strand	99-104	6	1
α-helix	111-124	14
β-strand	129-133	5	1
α-helix	141-152	12
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	220-229	10
α-helix	230-237	8
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

Chain B: 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	70-86	17
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	220-227	8
α-helix	228-236	9
β-strand	241-245	5	2
α-helix	247-249	3
α-helix	254-263	10
β-strand	267-271	5	2
β-strand	279-281	3	2
α-helix	284-291	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle protein	A, B	protein	297	THERMUS AQUATICUS	O07347 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1O87_1 SIGNAL RECOGNITION PARTICLE PROTEIN (chains A, B)
MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEAL
GKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLAL
YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEA
RDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT
GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (FMT, CL) are not listed.

Primary citation

Novel Protein and Mg2+ Configurations in the Mg2+Gdp Complex of the Srp Gtpase Ffh. Focia, P.J., Alam, H., Lu, T. et al. Proteins (2004) 54:222. DOI 10.1002/PROT.10598 · 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
1JPN 1.9 Å, GMPPNP Complex of SRP GTPase 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

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