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Crystal structure of apo human TUT1, form IV

Analyse Crystal structure of apo human TUT1, form IV in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WU6
Type: protein
Length: 1,589 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Speckle targeted PIP5K1A-regulated POLY(A) polymerase
EC: 2.7.7.19, 2.7.7.52
UniProt: Q9H6E5
Ligands: MG
Pockets: 17 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52)	protein	415	40% helix, 17% strand	Q9H6E5
B	Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52)	protein	413	40% helix, 17% strand	Q9H6E5
C	Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52)	protein	420	40% helix, 17% strand	Q9H6E5
D	Speckle targeted PIP5K1A-regulated POLY(A) polymerase (EC 2.7.7.19, 2.7.7.52)	protein	341	40% helix, 14% strand	Q9H6E5

Ligands and binding sites

MG · Magnesium ion · metal · 7 copies · chains A, B, D, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	532	0.66	0.77	60	MG
2	476	0.64	0.77	47	MG
3	495	0.63	0.76	45	empty
4	456	0.60	0.75	39	MG
5	393	0.59	0.76	38	MG

Interfaces

6 interfaces between chains.

C–D · 696 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 605 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 355 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 317 Å² buried · 1 hydrogen bond · protein-protein
A–D · 91 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5WU6 · Crystal structure of apo human Tut1, form IV · the same entry in another collection · chain D against D, TM-score 1.00
Q9H6E5 · AlphaFold monomer V2.0 prediction for speckle targeted PIP5K1A-regulated POLY(A)… · a predicted model of the same protein · chain D against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9H6E5
Elsewhere: RCSB PDB 5WU6 · PDBe 5WU6 · UniProt Q9H6E5

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