MolNFT v1 · #72670 · protein

Crystal structure of dimerization module of RNA polymerase I subcomplex A49/A34.5

3NFG · DNA-directed RNA polymerase I subunit RPA49: “Crystal structure of dimerization module of RNA polymerase I subcomplex A49/A34.5”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #72670 on GenesisL1: 3D structure…

PDB: 3NFG
Type: protein
Length: 1,716 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase I subunit RPA49; DNA-directed RNA polymerase I subunit RPA34
EC: 2.7.7.6
UniProt: Q6FNZ9, Q6FQI3
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 7% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, I, M, O	DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6)	protein	94	6% helix, 57% strand	Q6FNZ9
B, D, F, H, J, L, N	DNA-directed RNA polymerase I subunit RPA34 (EC 2.7.7.6)	protein	120	8% helix, 38% strand	Q6FQI3
C, G, K	DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6)	protein	95	6% helix, 56% strand	Q6FNZ9
E	DNA-directed RNA polymerase I subunit RPA49 (EC 2.7.7.6)	protein	96	6% helix, 55% strand	Q6FNZ9
P	DNA-directed RNA polymerase I subunit RPA34 (EC 2.7.7.6)	protein	119	8% helix, 38% strand	Q6FQI3

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1105	0.83	0.84	105	empty
2	589	0.79	0.85	63	empty
3	752	0.79	0.83	72	empty
4	1065	0.76	0.79	84	empty
5	693	0.73	0.79	57	empty

Interfaces

45 interfaces between chains.

E–G · 2941 Å² buried · 55 hydrogen bonds · protein-protein
A–O · 2897 Å² buried · 53 hydrogen bonds · protein-protein
K–M · 2870 Å² buried · 52 hydrogen bonds · protein-protein
C–I · 2832 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 1911 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

3NFG · Crystal structure of Dimerization module of RNA polymerase I subcomplex A49/A34.5 · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6FNZ9
Every structure of UniProt Q6FQI3
Elsewhere: RCSB PDB 3NFG · PDBe 3NFG · UniProt Q6FNZ9 · UniProt Q6FQI3

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