6LUR: Human PUF60 UHM domain

Human PUF60 UHM domain (thioredoxin fusion) in complex with a small molecule binder. Determined by X-ray diffraction at 2.0 Å resolution. Released 29 Apr 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Escherichia coli (strain K12), Homo sapiens
Chains: 8
Atoms: 13,950
Mol. weight: 199.63 kDa
Ligands: EVU
Released: 29 Apr 2020

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

Secondary structure: helices and β-sheets

6LUR contains 87 α-helices and 104 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: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	1
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	1
α-helix	377-392	16
β-strand	397-403	7	1
α-helix	411-414	4
β-strand	419	1	2
β-strand	421-426	6	1
β-strand	429-435	7	1
α-helix	440-451	12
β-strand	457	1	3
β-strand	460-464	5	4
α-helix	469-471	3
α-helix	476-484	9
α-helix	485-487	3
β-strand	490-500	11	4
β-strand	507-516	10	4
α-helix	519-529	11
β-strand	533-534	2	5
β-strand	537-538	2	5
β-strand	540-543	4	4
α-helix	546-550	5

Chain B: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	6
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	6
α-helix	377-392	16
β-strand	397-403	7	6
α-helix	411-414	4
β-strand	419	1	7
β-strand	421-426	6	6
β-strand	429-435	7	6
α-helix	440-452	13
β-strand	457	1	8
β-strand	460-464	5	9
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-500	11	9
α-helix	506	1
β-strand	507-516	10	9
α-helix	519-529	11
β-strand	533-534	2	10
β-strand	537-538	2	10
β-strand	540-544	5	9
α-helix	546-550	5

Chain C: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	348	1
β-strand	349-350	2	11
α-helix	351	1
α-helix	356	1
α-helix	357-361	5
β-strand	367-372	6	11
α-helix	377-392	16
β-strand	398-403	6	11
α-helix	411-414	4
β-strand	419	1	12
β-strand	421-426	6	11
β-strand	429-435	7	11
α-helix	440-452	13
β-strand	457	1	2
β-strand	460-464	5	13
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	13
β-strand	508-516	9	13
α-helix	519-529	11
β-strand	533-534	2	14
β-strand	537-538	2	14
α-helix	539	1
β-strand	540-543	4	13
α-helix	546-550	5

Chain D: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	349-351	3	15
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	15
α-helix	377-392	16
β-strand	397-403	7	15
α-helix	411-414	4
β-strand	419	1	16
β-strand	421-426	6	15
β-strand	429-435	7	15
α-helix	440-451	12
β-strand	457	1	7
β-strand	460-464	5	17
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-500	11	17
α-helix	506	1
β-strand	507-516	10	17
α-helix	519-529	11
β-strand	533-534	2	18
β-strand	537-538	2	18
α-helix	539	1
β-strand	540-544	5	17
α-helix	546-550	5

Chain E: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	348	1
β-strand	349-350	2	19
α-helix	351	1
α-helix	353-355	3
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	19
α-helix	377-392	16
β-strand	397-403	7	19
α-helix	411-414	4
β-strand	419	1	20
β-strand	421-426	6	19
β-strand	429-435	7	19
α-helix	440-452	13
β-strand	457	1	12
β-strand	460-464	5	21
α-helix	469-471	3
α-helix	476-484	9
α-helix	485-487	3
β-strand	490-499	10	21
β-strand	508-516	9	21
α-helix	519-529	11
β-strand	533-534	2	22
β-strand	537-538	2	22
β-strand	540-543	4	21
α-helix	546-550	5

Chain F: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	348-351	4	23
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	23
α-helix	377-392	16
β-strand	397-403	7	23
α-helix	411-414	4
β-strand	419	1	8
β-strand	421-426	6	23
β-strand	429-435	7	23
α-helix	440-452	13
β-strand	457	1	24
β-strand	460-464	5	25
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	25
α-helix	506-507	2
β-strand	508-516	9	25
α-helix	519-529	11
β-strand	533-534	2	26
β-strand	537-538	2	26
β-strand	540-543	4	25
α-helix	546-550	5

Chain G: 10 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	27
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	27
α-helix	377-392	16
β-strand	397-403	7	27
α-helix	411-414	4
β-strand	419	1	3
β-strand	421-426	6	27
β-strand	429-435	7	27
α-helix	440-451	12
α-helix	452-455	4
β-strand	457	1	20
β-strand	460-464	5	28
α-helix	469-471	3
α-helix	476-484	9
β-strand	490-499	10	28
β-strand	508-516	9	28
α-helix	519-529	11
β-strand	533-534	2	29
β-strand	537-538	2	29
β-strand	540-543	4	28
α-helix	546-550	5

Chain H: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	349-350	2	30
α-helix	356	1
α-helix	357-361	5
β-strand	366-372	7	30
α-helix	377-392	16
β-strand	398-403	6	30
α-helix	411-414	4
β-strand	419	1	24
β-strand	421-426	6	30
β-strand	429-435	7	30
α-helix	440-451	12
β-strand	457	1	16
β-strand	460-464	5	31
α-helix	469-471	3
α-helix	476-484	9
α-helix	485-487	3
β-strand	490-499	10	31
α-helix	506-507	2
β-strand	508-516	9	31
α-helix	519-529	11
β-strand	533-534	2	32
β-strand	537-538	2	32
β-strand	540-543	4	31
α-helix	546-550	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thioredoxin 1,Poly(U)-binding-splicing factor PUF60	A, B, C, D, E, F, G, H	protein	222	Escherichia coli (strain K12), Homo sapiens	P0AA25 (AlphaFold model), Q9UHX1 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>6LUR_1 Thioredoxin 1,Poly(U)-binding-splicing factor PUF60 (chains A, B, C, D, E, F, G, H)
MKHHHHHHPMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQ
GKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGS
AMESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFV
EFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLSA

Ligands and cofactors

ID	Name	Formula	Copies
EVU	4-[2-[4-(aminomethyl)phenyl]phenyl]piperazin-2-one	C17 H19 N3 O	8

Primary citation

Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery. Hanzawa, H., Shimada, T., Takahashi, M. et al. J Biomol NMR (2020) 74:501-508. DOI 10.1007/s10858-020-00314-0 · PubMed

Other PDB entries of the same protein (UniProt P0AA25 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HUA 1.1 Å, E. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue
5HR3 1.1 Å, Crystal structure of thioredoxin N106A mutant
5HR2 1.2 Å, Crystal structure of thioredoxin L94A mutant
5HR0 1.31 Å, Crystal structure of thioredoxin E101G mutant
4HU7 1.4 Å, E. coli thioredoxin variant with Pro76 as single proline residue
4HU9 1.55 Å, E. coli thioredoxin variant with (4S)-FluoroPro76 as single proline residue
4X43 1.65 Å, Structure of proline-free E. coli Thioredoxin
2TRX 1.68 Å, Crystal structure of thioredoxin from escherichia coli at 1.68 Å resolution
6Y4Y 1.75 Å, The crystal structure of human MACROD2 in space group P41212
1KEB 1.8 Å, Crystal Structure of Double Mutant M37L,P40S E.coli Thioredoxin
2EIQ 1.9 Å, Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal…
6Y4Z 1.9 Å, The crystal structure of human MACROD2 in space group P43212

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