4ITR: IbpAFic2-H3717A

Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Feb 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Haemophilus somnus, Homo sapiens
Chains: 4
Atoms: 8,384
Mol. weight: 115.57 kDa
Ligands: AMP, MG, GDP
Released: 20 Feb 2013

Explore 4ITR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ITR contains 60 α-helices and 24 β-strands across 4 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: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3499-3511	13
α-helix	3513	1
α-helix	3514-3518	5
α-helix	3521-3532	12
α-helix	3537-3543	7
α-helix	3549-3568	20
α-helix	3574-3585	12
α-helix	3593-3594	2
α-helix	3596-3609	14
α-helix	3612-3616	5
α-helix	3618-3635	18
α-helix	3642-3651	10
β-strand	3663	1	1
β-strand	3668-3669	2	2
β-strand	3673	1	3
α-helix	3678-3697	20
α-helix	3702-3716	15
β-strand	3719	1	1
α-helix	3723-3737	15
α-helix	3740-3743	4
α-helix	3751-3753	3
β-strand	3757	1	3
α-helix	3767-3779	13

Chain B: 18 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3499-3511	13
α-helix	3513	1
α-helix	3514-3518	5
α-helix	3521-3532	12
α-helix	3537-3543	7
α-helix	3549-3568	20
α-helix	3574-3586	13
α-helix	3593-3595	3
α-helix	3596-3609	14
α-helix	3612-3616	5
α-helix	3618-3635	18
α-helix	3642-3651	10
β-strand	3663	1	4
β-strand	3668-3669	2	5
β-strand	3673	1	6
α-helix	3678-3697	20
α-helix	3702-3716	15
β-strand	3719	1	4
α-helix	3723-3737	15
α-helix	3740-3743	4
α-helix	3751-3753	3
β-strand	3757	1	6
α-helix	3767-3779	13

Chain C: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	7
α-helix	16-25	10
β-strand	33-34	2	5
α-helix	37-39	3
β-strand	40-46	7	7
β-strand	49-56	8	7
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	7
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	7
α-helix	117-121	5
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	7
α-helix	165-177	13

Chain D: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	8
α-helix	16-25	10
β-strand	33-34	2	2
α-helix	37-39	3
β-strand	40-46	7	8
β-strand	49-56	8	8
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	8
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	8
α-helix	117-121	5
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-148	10
β-strand	154-156	3	8
α-helix	165-176	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenosine monophosphate-protein transferase and cysteine protease IbpA	A, B	protein	316	Haemophilus somnus	Q06277
Cell division control protein 42 homolog	C, D	protein	191	Homo sapiens	P60953 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4ITR_1 Adenosine monophosphate-protein transferase and cysteine protease IbpA (chains A, B)
DETANKVNYQDLEDNLNLKGLISLEDDRNANFESNVLKNEKFLDEAREISKKSIPEATVK
QMSHLPEFDDILTEGAKKVESRINKAITFRPSVEEFSEIQDLVKTLPKTKVIEDLSTKTN
EITEALAATSKTIQRTPELKEQLKTAIEDFLQNSQGKPLTVQMIENLNHGLRPDEGEGRL
LYKKENLTKENAVFSSPEAAKIQLAETVDFINRAKNEGIEPSVVGALVYQRLIAYAPFAE
GNGRMARVIVNKILLDAGYPAFTKFSDEFEPQIIPQTKASTKSATSSEVVVEFLKELAKK
GSKEDNEQNLEKTDRT

Sequence of entity 2 (C, D), FASTA

>4ITR_2 Cell division control protein 42 homolog (chains C, D)
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAG
QEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLR
DDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEPP
EPKKSRRCVLL

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural basis of Fic-mediated adenylylation. Xiao, J., Worby, C.A., Mattoo, S. et al. Nat Struct Mol Biol (2010) 17:1004-1010. DOI 10.1038/nsmb.1867 · PubMed

Other PDB entries of the same protein (UniProt Q06277), best resolution first:

3N3U 1.85 Å, Crystal Structure of IbpAFic2
6SIU 2.49 Å, Crystal structure of IbpAFic2 covalently tethered to Cdc42

Browse structure collections

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