MolNFT v1 · #146247 · protein + DNA

Cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas

6DBV · Recombination activating gene 1 - mbp chimera: “Cryo-EM structure of rag in complex with 12-rss and 23-rss substrate dnas”. Electron microscopy, 2 ligands (CA, ZN), 20 pockets (best druggability 0.87). MolNFT v1 #146247 on…

PDB: 6DBV
Type: protein + DNA
Length: 2,161 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Recombination activating gene 1 - mbp chimera; Recombination activating gene 2; Forward…
EC: 2.3.2.27
UniProt: P0AEX9, O13033, Q1RLW7
Ligands: CA, ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 7 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Recombination activating gene 1 - mbp chimera (EC 2.3.2.27)	protein	616	48% helix, 10% strand	P0AEX9, O13033
B, D	Recombination activating gene 2	protein	351	3% helix, 40% strand	Q1RLW7
C	Recombination activating gene 1 - mbp chimera (EC 2.3.2.27)	protein	621	48% helix, 9% strand	P0AEX9, O13033
E	Forward strand of 12-rss substrate DNA	dna	50	—	—
F	Reverse strand of 12-rss substrate DNA	dna	50	—	—
G	Forward strand of 23-rss substrate DNA	dna	61	—	—
H	Reverse strand of 23-rss substrate DNA	dna	61	—	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, E, C, H
ZN · Zinc ion · metal · 2 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	871	0.87	0.89	74	empty
2	776	0.86	0.89	81	empty
3	906	0.85	0.86	84	empty
4	297	0.78	0.90	44	empty
5	1178	0.75	0.78	92	CA

Interfaces

17 interfaces between chains.

A–C · 3417 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2790 Å² buried · 227 hydrogen bonds · nucleic-nucleic
E–F · 2186 Å² buried · 185 hydrogen bonds · nucleic-nucleic
A–B · 1846 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1844 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6DBV · Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs · the same entry in another collection · chain H against H, TM-score 1.00
O13033 · AlphaFold monomer V2.0 prediction for V(D)J recombination-activating protein 1 (O13033) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 P0AEX9
Every structure of UniProt O13033
Every structure of UniProt Q1RLW7
Elsewhere: RCSB PDB 6DBV · PDBe 6DBV · UniProt P0AEX9 · UniProt O13033 · UniProt Q1RLW7

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