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Structure of E. COLI MS115-1 nucc, 5'-papa bound form

Analyse Structure of E. COLI MS115-1 nucc, 5'-papa bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6P7Q
Type: protein + RNA
Length: 728 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E. COLI MS115-1 nucc; RNA (5'-R(P*AP*A)-3')
UniProt: D7Y2H5
Ligands: CL
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E. COLI MS115-1 nucc	protein	240	38% helix, 28% strand	D7Y2H5
B	E. COLI MS115-1 nucc	protein	240	36% helix, 28% strand	D7Y2H5
C	E. COLI MS115-1 nucc	protein	242	37% helix, 28% strand	D7Y2H5
D, E, F	RNA (5'-R(PAPA)-3')	rna	2	—	—

Ligands and binding sites

CL · Chloride ion · ion · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	644	0.66	0.75	68	empty
2	400	0.63	0.77	52	CL
3	56	0.28	0.73	11	empty

Interfaces

5 interfaces between chains.

A–C · 823 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 398 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 327 Å² buried · 3 hydrogen bonds · protein-nucleic
C–F · 324 Å² buried · 3 hydrogen bonds · protein-nucleic
A–D · 319 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6P7Q · Structure of E. coli MS115-1 NucC, 5'-pApA bound form · the same entry in another collection · chain A against A, TM-score 1.00
D7Y2H5 · AlphaFold monomer V2.0 prediction for endodeoxyribonuclease nucc (D7Y2H5) · a predicted model of the same protein · chain A 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 D7Y2H5
Elsewhere: RCSB PDB 6P7Q · PDBe 6P7Q · UniProt D7Y2H5

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