MolNFT v1 · #162073 · protein + DNA

CAS1-CAS2-CSN2-DNA dimer complex from the type II-a CRISPR-CAS system

6QXT · CRISPR-associated protein CSN2: “CAS1-CAS2-CSN2-DNA dimer complex from the type II-a CRISPR-CAS system”. Electron microscopy, 1 ligand (CA), 20 pockets (best druggability 0.83). MolNFT v1 #162073 on GenesisL1: 3D structure, binding…

PDB: 6QXT
Type: protein + DNA
Length: 11,672 residues
Chains: 54
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CRISPR-associated protein CSN2; CRISPR-associated endonuclease CAS1; CRISPR-associated…
EC: 3.1.-.-
UniProt: G3ECR4, G3ECR2, G3ECR3
Ligands: CA
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 7 distinct chains · 42% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G, a, c, e, g	CRISPR-associated protein CSN2	protein	218	42% helix, 18% strand	G3ECR4
B, D, F, H, b, d, f, h	CRISPR-associated protein CSN2	protein	219	41% helix, 18% strand	G3ECR4
I, J, L, M, O, P, R, S, U, V, Y, Z, i, j, l, m, o, p, r, s, u, v, y, z	CRISPR-associated endonuclease CAS1 (EC 3.1.-.-)	protein	287	49% helix, 17% strand	G3ECR2
K, N, Q, T, k, n, q, t	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	96	36% helix, 32% strand	G3ECR3
W, X, w, x	CRISPR-associated endoribonuclease CAS2 (EC 3.1.-.-)	protein	103	34% helix, 30% strand	G3ECR3
1	DNA (64-mer)	dna	54	—	—
2	DNA (64-mer)	dna	54	—	—

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, D, B, C, E, H, F, G, a, d, b, c, e, h, f, g

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	1001	0.83	0.84	108	empty
2	794	0.83	0.86	108	empty
3	760	0.83	0.87	95	empty
4	961	0.83	0.84	102	empty
5	1177	0.83	0.84	126	empty

Interfaces

125 interfaces between chains.

1–2 · 2239 Å² buried · 163 hydrogen bonds · nucleic-nucleic
q–t · 915 Å² buried · 16 hydrogen bonds · protein-protein
K–N · 914 Å² buried · 16 hydrogen bonds · protein-protein
k–n · 911 Å² buried · 16 hydrogen bonds · protein-protein
Q–T · 909 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6QXT · Cas1-Cas2-Csn2-DNA dimer complex from the Type II-A CRISPR-Cas system · the same entry in another collection · chain J against J, 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 G3ECR4
Every structure of UniProt G3ECR2
Every structure of UniProt G3ECR3
Elsewhere: RCSB PDB 6QXT · PDBe 6QXT · UniProt G3ECR4 · UniProt G3ECR2 · UniProt G3ECR3

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