6SIU: IbpAFic2 covalently tethered to Cdc42

Crystal structure of IbpAFic2 covalently tethered to Cdc42. Determined by X-ray diffraction at 2.49 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 2.49 Å
Organisms: Histophilus somni (strain 2336), Homo sapiens
Chains: 4
Atoms: 7,816
Mol. weight: 116.4 kDa
Ligands: GDP, LJN
Released: 18 Mar 2020

Explore 6SIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SIU contains 64 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: 19 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3499-3511	13
α-helix	3513	1
α-helix	3514-3518	5
α-helix	3521-3533	13
α-helix	3537-3543	7
α-helix	3549-3568	20
α-helix	3574-3585	12
α-helix	3593-3594	2
α-helix	3596-3610	15
α-helix	3612-3616	5
α-helix	3618-3634	17
α-helix	3642-3651	10
β-strand	3663	1	1
β-strand	3668-3670	3	2
β-strand	3673-3674	2	2
α-helix	3678-3697	20
α-helix	3702-3716	15
β-strand	3719	1	1
α-helix	3723-3736	14
α-helix	3740-3743	4
α-helix	3751-3753	3
β-strand	3757	1	2
α-helix	3763-3766	4
α-helix	3767-3780	14

Chain B: 19 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	3596-3610	15
α-helix	3612-3616	5
α-helix	3618-3634	17
α-helix	3642-3651	10
β-strand	3663	1	3
β-strand	3668-3670	3	4
β-strand	3673-3674	2	4
α-helix	3678-3697	20
α-helix	3702-3716	15
β-strand	3719	1	3
α-helix	3723-3738	16
α-helix	3740-3743	4
α-helix	3751-3753	3
β-strand	3757	1	4
α-helix	3763-3766	4
α-helix	3767-3783	17

Chain C: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
α-helix	16-25	10
α-helix	28-30	3
β-strand	33-34	2	4
α-helix	37-39	3
β-strand	40-46	7	5
β-strand	49-57	9	5
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	5
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	5
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	5
α-helix	165-176	12

Chain D: 13 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
α-helix	16-25	10
α-helix	32	1
β-strand	33-34	2	2
α-helix	37-39	3
β-strand	40-44	5	6
β-strand	51-57	7	6
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	6
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	6
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	6
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein adenylyltransferase and cysteine protease IbpA	A, B	protein	316	Histophilus somni (strain 2336)	Q06277
Cell division control protein 42 homolog	C, D	protein	192	Homo sapiens	P60953 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6SIU_1 Protein adenylyltransferase and cysteine protease IbpA (chains A, B)
GETANKVNYQDLEDNLNLKGLISLEDDRNANFESNVLKNEKFLDEAREISKKSIPEATVK
QMSHLPEFDDILTEGAKKVESRINKAITFRPSVEEFSEIQDLVKTLPKTKVIEDLSTKTN
EITEALAATSKTIQRTPELKEQLKTAIEDFLQNSQGKPLTVQMIENLNHGLRPDEGEGRL
LYKKENLTKENAVFSSPEAAKIQLAETVDFINRAKNEGIEPSVVGALVYQRLIAYHPFAE
GNGRMARVIVNKILLDAGYPAFTKFSDEFEPQICPQTKASTKSATSSEVVVEFLKELAKK
GSKEDNEQNLEKTDRT

Sequence of entity 2 (C, D), FASTA

>6SIU_2 Cell division control protein 42 homolog (chains C, D)
GMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTA
GQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDL
RDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEP
PEPKKSRRCVLL

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
LJN	[(2~{R},3~{S},4~{R},5~{R})-5-[4-(acetamidomethyl)-1,2,3-triazol-1-yl]-3,4-bis(o…	C10 H17 N4 O8 P	2

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

Primary citation

Identification of targets of AMPylating Fic enzymes by co-substrate-mediated covalent capture. Gulen, B., Rosselin, M., Fauser, J. et al. Nat Chem (2020) 12:732-739. DOI 10.1038/s41557-020-0484-6 · PubMed

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

3N3U 1.85 Å, Crystal Structure of IbpAFic2
4ITR 2.3 Å, Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42

Browse structure collections

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