MolNFT v1 · #153023 · protein

Crystal structure of yeast RTT107 and MMS22

6J0X · Regulator of TY1 transposition protein 107: “Crystal structure of yeast RTT107 and MMS22”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #153023 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6J0X
Type: protein
Length: 1,920 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulator of TY1 transposition protein 107; Peptide from E3 ubiquitin-protein ligase…
UniProt: P38850, Q06164
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 39% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulator of TY1 transposition protein 107	protein	465	39% helix, 13% strand	P38850
E, F, G, H	Peptide from E3 ubiquitin-protein ligase substrate receptor MMS22	protein	16	19% helix, 19% strand	Q06164
B	Regulator of TY1 transposition protein 107	protein	466	38% helix, 14% strand	P38850
C	Regulator of TY1 transposition protein 107	protein	463	40% helix, 14% strand	P38850
D	Regulator of TY1 transposition protein 107	protein	462	39% helix, 14% strand	P38850

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1156	0.84	0.85	117	empty
2	99	0.79	0.99	18	empty
3	103	0.79	0.98	19	empty
4	95	0.79	0.99	17	empty
5	97	0.78	0.98	19	empty

Interfaces

7 interfaces between chains.

A–B · 1134 Å² buried · 14 hydrogen bonds · protein-protein
A–E · 966 Å² buried · 17 hydrogen bonds · protein-protein
C–G · 955 Å² buried · 16 hydrogen bonds · protein-protein
B–F · 950 Å² buried · 18 hydrogen bonds · protein-protein
D–H · 940 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6J0X · Crystal Structure of Yeast Rtt107 and Mms22 · the same entry in another collection · chain H against H, TM-score 1.00
P38850 · AlphaFold monomer V2.0 prediction for regulator of TY1 transposition protein 107 (P38850) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P38850
Every structure of UniProt Q06164
Elsewhere: RCSB PDB 6J0X · PDBe 6J0X · UniProt P38850 · UniProt Q06164

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