MolNFT v1 · #147323 · protein + RNA

ESCAS13D-crrna-target RNA ternary complex

6E9F: “ESCAS13D-crrna-target RNA ternary complex”. Electron microscopy, 1 ligand (MG), 17 pockets (best druggability 0.82). MolNFT v1 #147323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6E9F
Type: protein + RNA
Length: 943 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ESCAS13D; Crrna (52-mer); RNA (27-mer)
UniProt: B0MS50
Ligands: MG
Pockets: 17 · best druggability 0.82

Structure

electron microscopy · 3 distinct chains · 47% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ESCAS13D	protein	864	47% helix, 5% strand	B0MS50
B	Crrna (52-mer)	rna	52	—	—
C	RNA (27-mer)	rna	27	—	—

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.82	0.83	80	empty
2	948	0.76	0.80	67	empty
3	54	0.68	0.97	21	empty
4	736	0.64	0.74	56	empty
5	280	0.61	0.80	22	empty

Interfaces

3 interfaces between chains.

A–B · 3463 Å² buried · 78 hydrogen bonds · protein-nucleic
A–C · 1205 Å² buried · 19 hydrogen bonds · protein-nucleic
B–C · 1039 Å² buried · 104 hydrogen bonds · nucleic-nucleic

Compared structures

6E9F · EsCas13d-crRNA-target RNA ternary complex · the same entry in another collection · chain B against B, 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 B0MS50
Elsewhere: RCSB PDB 6E9F · PDBe 6E9F · UniProt B0MS50

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