MolNFT v1 · #174356 · protein

ECOR124I-ocr in the intermediate state

7BST · Type I restriction enzyme R protein: “ECOR124I-ocr in the intermediate state”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #174356 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7BST
Type: protein
Length: 3,508 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type I restriction enzyme R protein; Type I restriction enzyme ECOR124II M protein…
EC: 3.1.21.3, 2.1.1.72
UniProt: Q304R3, P10484, P03775, P10485
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 6 distinct chains · 39% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Type I restriction enzyme R protein (EC 3.1.21.3)	protein	975	43% helix, 11% strand	Q304R3
C	Type I restriction enzyme R protein (EC 3.1.21.3)	protein	992	43% helix, 11% strand	Q304R3
D	Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72)	protein	472	32% helix, 7% strand	P10484
E	Type I restriction enzyme ECOR124II M protein (EC 2.1.1.72)	protein	473	33% helix, 6% strand	P10484
F, G	Overcome classical restriction GP0.3	protein	106	64% helix, 0% strand	P03775
A	Type-1 restriction enzyme ECOR124II specificity protein	protein	384	28% helix, 14% strand	P10485

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	1128	0.87	0.88	161	empty
2	776	0.84	0.87	85	empty
3	201	0.80	0.94	36	empty
4	518	0.79	0.85	83	empty
5	1058	0.79	0.80	100	empty

Interfaces

15 interfaces between chains.

B–D · 1835 Å² buried · 16 hydrogen bonds · protein-protein
E–A · 1494 Å² buried · 13 hydrogen bonds · protein-protein
D–A · 1402 Å² buried · 7 hydrogen bonds · protein-protein
C–E · 1096 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 915 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7BST · EcoR124I-Ocr in the Intermediate State · the same entry in another collection · chain A against A, TM-score 1.00
P10484 · AlphaFold monomer V2.0 prediction for type I restriction enzyme ECOR124II M protein… · a predicted model of the same protein · chain D against A, TM-score 0.94
P10485 · AlphaFold monomer V2.0 prediction for type-1 restriction enzyme ECOR124II specificity… · a predicted model of the same protein · chain A against A, TM-score 0.88

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 Q304R3
Every structure of UniProt P10484
Every structure of UniProt P03775
Every structure of UniProt P10485
Elsewhere: RCSB PDB 7BST · PDBe 7BST · UniProt Q304R3 · UniProt P10484 · UniProt P03775 · UniProt P10485

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