5A5H: Bifunctional glutamate/proline--tRNA ligase

The crystal structure of the GST-like domains complex of EPRS C92SC105SC123S mutant-AIMP2. Determined by X-ray diffraction at 2.32 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 2.32 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 11,755
Mol. weight: 184.78 kDa
Released: 29 Jun 2016

Explore 5A5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5A5H contains 81 α-helices and 44 β-strands across 8 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: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	15-22	8
β-strand	30-33	4	1
β-strand	36-43	8	1
β-strand	46-48	3	1
α-helix	51-61	11
α-helix	72-86	15
α-helix	88-91	4
α-helix	95-106	12
α-helix	119-129	11
α-helix	132-138	7
α-helix	145-156	12
α-helix	158-167	10

Chain B: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	121-126	6	2
α-helix	133-143	11
β-strand	148-155	8	2
α-helix	163-166	4
β-strand	183-189	7	2
β-strand	196-198	3	2
α-helix	205-206	2
β-strand	207-208	2	2
α-helix	210-219	10
α-helix	227-239	13
α-helix	240-244	5
α-helix	249-262	14
β-strand	268	1	3
β-strand	271	1	3
α-helix	276-286	11
α-helix	297-307	11
α-helix	310-318	9

Chain C: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
α-helix	15-24	10
β-strand	30-33	4	4
β-strand	39-43	5	4
β-strand	46-48	3	4
α-helix	51-61	11
α-helix	63-65	3
α-helix	72-86	15
α-helix	95-106	12
α-helix	119-130	12
α-helix	132-139	8
α-helix	145-155	11
α-helix	158-167	10

Chain D: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	108-112	5
α-helix	113-115	3
α-helix	116-119	4
β-strand	121-126	6	5
α-helix	133-145	13
β-strand	148-154	7	5
α-helix	163-166	4
α-helix	180-181	2
β-strand	183-189	7	5
β-strand	196-198	3	5
β-strand	207-208	2	5
α-helix	210-219	10
α-helix	227-239	13
α-helix	240-244	5
α-helix	249-262	14
β-strand	268	1	6
β-strand	271	1	6
α-helix	276-288	13
α-helix	294-296	3
α-helix	297-307	11
α-helix	310-317	8

Chains E and G: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
α-helix	15-24	10
β-strand	30-35	6	7
β-strand	39-43	5	7
β-strand	46-48	3	7
α-helix	51-61	11
α-helix	63-65	3
α-helix	72-86	15
α-helix	95-106	12
α-helix	119-129	11
α-helix	132-139	8
α-helix	145-155	11
α-helix	158-167	10

Chain F: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	121-126	6	2
α-helix	133-143	11
β-strand	148-155	8	2
α-helix	163-166	4
β-strand	183-189	7	2
β-strand	196-198	3	2
β-strand	207-208	2	2
α-helix	210-219	10
α-helix	227-238	12
α-helix	239-244	6
α-helix	249-262	14
β-strand	268	1	8
β-strand	271	1	8
α-helix	276-287	12
α-helix	293-296	4
α-helix	297-307	11
α-helix	310-317	8

Chain H: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	121-125	5	10
α-helix	133-145	13
β-strand	148-154	7	10
α-helix	163-166	4
β-strand	183-189	7	10
β-strand	196-198	3	10
α-helix	205-206	2
β-strand	207-208	2	10
α-helix	210-219	10
α-helix	227-238	12
α-helix	239-244	6
α-helix	249-265	17
β-strand	268	1	11
β-strand	271	1	11
α-helix	276-287	12
α-helix	294-296	3
α-helix	297-307	11
α-helix	310-317	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Bifunctional glutamate/proline--tRNA ligase	A, C, E, G	protein	175	HOMO SAPIENS	P07814 (AlphaFold model)
Aminoacyl tRNA synthase complex-interacting multifunctiona L protein 2	B, D, F, H	protein	240	HOMO SAPIENS	Q13155 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5A5H_1 BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE (chains A, C, E, G)
MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLAR
VATTAGLYGSNLMEHTEIDHWLEFSATKLSSSDSFTSTINELNHSLSLRTYLVGNSLSLA
DLSVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVSTTKAR

Sequence of entity 2 (B, D, F, H), FASTA

>5A5H_2 AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONA L PROTEIN 2 (chains B, D, F, H)
MTNIIQADEPTTLTTNALDLNSVLGKDYGALKDIVINANPASPPLSLLVLHRLLCEHFRV
LSTVHTHSSVKSVPENLLKCFGEQNKKQPRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIE
GEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPW
LAGNELTVADVVLWSVLQQIGGCSVTVPANVQRWMRSCENLAPFNTALKLLKLEHHHHHH

Primary citation

The Crystal Structure of the Gst-Like Domains Complex of Eprs C92Sc105Sc123S Mutant-Aimp2. Cho, H.Y., Kang, B.S. To be published.

Other PDB entries of the same protein (UniProt P07814 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7X09 1.7 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with inhibitors L95 and…
7F99 1.98 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
7Y1H 1.99 Å, Controlling fibrosis using compound with novel binding mode to prolyl-tRNA synthetase 1
7F9B 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
7F98 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L95
7F9A 2.0 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L97
4HVC 2.0 Å, Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP…
7X1O 2.04 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with double inhibitors HF and L95
5A1N 2.1 Å, The crystal structure of the GST-like domains complex of EPRS-AIMP2 mutant S156D
7BBU 2.19 Å, Crystal Structure of human Prolyl-tRNA synthetase in complex with NCP26 and L-Proline
7F9C 2.2 Å, Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96
7OSY 2.23 Å, Human Prolyl-tRNA Synthetase in Complex with L-proline

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