MolNFT v1 · #163973 · protein + DNA

Cryo-EM structure of the recbcd chi recognised complex

6SJB · Recbcd enzyme subunit recb: “Cryo-EM structure of the recbcd chi recognised complex”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #163973 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SJB
Type: protein + DNA
Length: 2,915 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Recbcd enzyme subunit recb; Recbcd enzyme subunit recc; Recbcd enzyme subunit recd; DNA…
EC: 3.1.11.5
UniProt: A0A024LB08, P07648, A0A061K747
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 4 distinct chains · 45% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Recbcd enzyme subunit recb (EC 3.1.11.5)	protein	1129	47% helix, 13% strand	A0A024LB08
C	Recbcd enzyme subunit recc (EC 3.1.11.5)	protein	1121	45% helix, 11% strand	P07648
D	Recbcd enzyme subunit recd (EC 3.1.11.5)	protein	597	42% helix, 14% strand	A0A061K747
X	DNA fork substrate	dna	68	—	—

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	832	0.87	0.89	82	empty
2	605	0.80	0.85	60	empty
3	721	0.79	0.84	59	empty
4	492	0.78	0.86	71	empty
5	388	0.75	0.85	60	empty

Interfaces

6 interfaces between chains.

B–C · 7310 Å² buried · 79 hydrogen bonds · protein-protein
C–X · 2476 Å² buried · 46 hydrogen bonds · protein-nucleic
B–X · 2266 Å² buried · 30 hydrogen bonds · protein-nucleic
C–D · 1482 Å² buried · 12 hydrogen bonds · protein-protein
D–X · 1074 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

6SJB · Cryo-EM structure of the RecBCD Chi recognised complex · the same entry in another collection · chain B against B, TM-score 1.00
P07648 · AlphaFold monomer V2.0 prediction for recbcd enzyme subunit recc (P07648) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 A0A024LB08
Every structure of UniProt P07648
Every structure of UniProt A0A061K747
Elsewhere: RCSB PDB 6SJB · PDBe 6SJB · UniProt A0A024LB08 · UniProt P07648 · UniProt A0A061K747

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