2Q7U: Protein traI

Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base and Imidodiphosphate. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 May 2008.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Escherichia coli
Chains: 2
Atoms: 4,203
Mol. weight: 67.23 kDa
Ligands: TMP, PON, MG
Released: 20 May 2008

Explore 2Q7U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Q7U contains 29 α-helices and 26 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	10-18	9
α-helix	20-23	4
β-strand	32-34	3	1
α-helix	36-39	4
α-helix	49-57	9
β-strand	59	1	2
β-strand	65	1	2
β-strand	69-70	2	3
β-strand	73-74	2	3
β-strand	79-85	7	1
α-helix	86-87	2
α-helix	88-95	8
α-helix	100-119	20
β-strand	122-125	4	4
β-strand	132-135	4	4
β-strand	140-146	7	1
β-strand	157-163	7	1
β-strand	166-168	3	5
β-strand	171-173	3	5
α-helix	174-176	3
α-helix	185-190	6
α-helix	193-209	17
β-strand	216-217	2	6
α-helix	220-222	3
β-strand	224-225	2	6
α-helix	231-234	4
α-helix	270-282	13
α-helix	288-298	11

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1002-1006	5	7
α-helix	1010-1018	9
α-helix	1020-1022	3
β-strand	1032-1034	3	7
α-helix	1035-1039	5
α-helix	1049-1056	8
β-strand	1079-1085	7	7
α-helix	1086-1087	2
α-helix	1088-1091	4
α-helix	1092-1096	5
α-helix	1101-1117	17
α-helix	1118-1120	3
β-strand	1122-1123	2	8
α-helix	1127-1129	3
β-strand	1134-1135	2	8
β-strand	1141-1148	8	7
β-strand	1154-1163	10	7
β-strand	1168	1	9
β-strand	1171	1	9
α-helix	1185-1191	7
α-helix	1193-1210	18
β-strand	1216-1217	2	10
β-strand	1224-1225	2	10
α-helix	1232-1234	3
α-helix	1270-1282	13
α-helix	1288-1299	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein traI	A, B	protein	301	Escherichia coli	P14565 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2Q7U_1 Protein traI (chains A, B)
MMSIAQVRSAGSAGNFYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRL
PDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL
ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKV
GKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQT
IREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD
S

Ligands and cofactors

ID	Name	Formula	Copies
TMP	Thymidine-5'-phosphate	C10 H15 N2 O8 P	1
PON	Imido diphosphate	H3 N O6 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Disrupting antibiotic resistance propagation by inhibiting the conjugative DNA relaxase. Lujan, S.A., Guogas, L.M., Ragonese, H. et al. Proc Natl Acad Sci U S A (2007) 104:12282-12287. DOI 10.1073/pnas.0702760104 · PubMed

Other PDB entries of the same protein (UniProt P14565 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FLD 2.4 Å, Crystal structure of the trai c-terminal domain
2Q7T 2.42 Å, Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base
1P4D 2.6 Å, F factor TraI Relaxase Domain
2A0I 2.72 Å, F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA
9F10 2.94 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, without accessory…
9F0Z 3.42 Å, CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode,…
9F12 3.42 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_-3ds-2_+143 and TraI…
9F0Y 3.45 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the…
9F11 3.68 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI…
9F0X 3.78 Å, CryoEM structure of the F plasmid relaxosome in its pre-initiation state, derived from…
2L8B TraI (381-569)

Browse structure collections

About this viewer

MolViewer shows 2Q7U 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.