MolNFT v1 · #140479 · protein

Crystal structure of inner membrane protein BQT4 in complex with telomeric protein RAP1

5YC2 · Ubiquitin-like protein SMT3,BOUQUET formation protein 4: “Crystal structure of inner membrane protein BQT4 in complex with telomeric protein RAP1”. X-ray diffraction, 5 pockets (best druggability 0.69). MolNFT v1 #140479 on…

PDB: 5YC2
Type: protein
Length: 431 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ubiquitin-like protein SMT3,BOUQUET formation protein 4; DNA-binding protein RAP1
UniProt: Q12306, O60158, Q96TL7
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ubiquitin-like protein SMT3,BOUQUET formation protein 4	protein	202	30% helix, 30% strand	Q12306, O60158
B	DNA-binding protein RAP1	protein	14	64% helix, 0% strand	Q96TL7
C	Ubiquitin-like protein SMT3,BOUQUET formation protein 4	protein	200	31% helix, 29% strand	Q12306, O60158
D	DNA-binding protein RAP1	protein	15	80% helix, 0% strand	Q96TL7

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	703	0.69	0.77	59	empty
2	205	0.50	0.76	29	empty
3	145	0.42	0.75	29	empty
4	80	0.36	0.76	14	empty
5	57	0.26	0.73	11	empty

Interfaces

4 interfaces between chains.

A–B · 622 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 545 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 366 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 40 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YC2 · Crystal structure of inner membrane protein Bqt4 in complex with telomeric protein Rap1 · the same entry in another collection · chain A against A, TM-score 1.00
Q96TL7 · AlphaFold monomer V2.0 prediction for DNA-binding protein RAP1 (Q96TL7) · a predicted model of the same protein · chain D against A, TM-score 0.78
O60158 · AlphaFold monomer V2.0 prediction for bouquet formation protein 4 (O60158) · a predicted model of the same protein · chain C against A, TM-score 0.67
Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain A against A, TM-score 0.38

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 Q12306
Every structure of UniProt O60158
Every structure of UniProt Q96TL7
Elsewhere: RCSB PDB 5YC2 · PDBe 5YC2 · UniProt Q12306 · UniProt O60158 · UniProt Q96TL7

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