MolNFT v1 · #139636 · protein + RNA

Anti-CRISPR proteins ACRF1/2 bound to csy surveillance complex with a 20NT spacer crrna backbone region

5XLP · CRISPR-associated protein CSY3: “Anti-CRISPR proteins ACRF1/2 bound to csy surveillance complex with a 20NT spacer crrna backbone region”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #139636 on GenesisL1: 3D…

PDB: 5XLP
Type: protein + RNA
Length: 1,367 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated protein CSY3; Crrna with 20NT spacer sequence; Uncharacterized protein…
UniProt: Q02MM1, L7P7M1
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 4 distinct chains · 24% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	CRISPR-associated protein CSY3	protein	287	24% helix, 11% strand	Q02MM1
D, E, F	CRISPR-associated protein CSY3	protein	326	24% helix, 13% strand	Q02MM1
K	Crrna with 20NT spacer sequence	rna	24	—	—
M	Uncharacterized protein ACRF1	protein	78	27% helix, 17% strand	L7P7M1

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.89	0.91	134	empty
2	1012	0.88	0.89	123	empty
3	835	0.88	0.91	121	empty
4	499	0.84	0.90	90	empty
5	471	0.75	0.83	45	empty

Interfaces

10 interfaces between chains.

D–E · 1628 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1620 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1508 Å² buried · 5 hydrogen bonds · protein-protein
E–K · 1015 Å² buried · 14 hydrogen bonds · protein-nucleic
D–K · 983 Å² buried · 15 hydrogen bonds · protein-nucleic

Compared structures

5XLP · Anti-CRISPR proteins AcrF1/2 bound to Csy surveillance complex with a 20nt spacer crRNA… · the same entry in another collection · chain M against M, TM-score 1.00
Q02MM1 · AlphaFold monomer V2.0 prediction for CRISPR-associated protein CSY3 (Q02MM1) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q02MM1
Every structure of UniProt L7P7M1
Elsewhere: RCSB PDB 5XLP · PDBe 5XLP · UniProt Q02MM1 · UniProt L7P7M1

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