MolNFT v1 · #129020 · protein

Crystal structure of S. cerevisiae core factor at 3.2A resolution

5O7X · RNA polymerase I-specific transcription initiation factor…: “Crystal structure of S. cerevisiae core factor at 3.2A resolution”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.88). MolNFT v1 #129020 on…

PDB: 5O7X
Type: protein
Length: 7,668 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA polymerase I-specific transcription initiation factor RRN6; RNA polymerase I-specific…
UniProt: P32786, P40992, Q04712
Ligands: MG, SO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, G, J, M, P	RNA polymerase I-specific transcription initiation factor RRN6	protein	598	24% helix, 28% strand	P32786
B, E, H, K, N, Q	RNA polymerase I-specific transcription initiation factor RRN7	protein	377	59% helix, 0% strand	P40992
C, F, I, L, O, R	RNA polymerase I-specific transcription initiation factor RRN11	protein	303	60% helix, 1% strand	Q04712

Ligands and binding sites

MG · Magnesium ion · metal · 6 copies · chains A, C, D, F, G, I, J, L, M, O, P, R
SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	989	0.88	0.89	116	empty
2	863	0.87	0.89	109	SO4
3	750	0.86	0.89	90	empty
4	776	0.85	0.88	91	empty
5	750	0.85	0.88	90	empty

Interfaces

33 interfaces between chains.

A–B · 4383 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 4383 Å² buried · 34 hydrogen bonds · protein-protein
D–E · 4381 Å² buried · 34 hydrogen bonds · protein-protein
M–N · 4376 Å² buried · 34 hydrogen bonds · protein-protein
P–Q · 4371 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

P40992 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain B against A, TM-score 0.93
P32786 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain A against A, TM-score 0.89
Q04712 · AlphaFold monomer V2.0 prediction for RNA polymerase I-specific transcription initiation… · a predicted model of the same protein · chain C against A, TM-score 0.70

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 P32786
Every structure of UniProt P40992
Every structure of UniProt Q04712
Elsewhere: RCSB PDB 5O7X · PDBe 5O7X · UniProt P32786 · UniProt P40992 · UniProt Q04712

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