MolNFT v1 · #26850 · protein

Water-mediate interaction at aprotein-protein interface

1X1X · Ribonuclease: “Water-mediate interaction at aprotein-protein interface”. X-ray diffraction, 4 pockets (best druggability 0.64). MolNFT v1 #26850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1X1X
Type: protein
Length: 596 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonuclease; Barstar
EC: 3.1.27.-
UniProt: P00648, P11540
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ribonuclease (EC 3.1.27.-)	protein	110	22% helix, 23% strand	P00648
C	Ribonuclease (EC 3.1.27.-)	protein	109	23% helix, 23% strand	P00648
D, E, F	Barstar	protein	89	51% helix, 18% strand	P11540

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.64	0.75	62	empty
2	339	0.55	0.75	34	empty
3	134	0.44	0.76	23	empty
4	70	0.39	0.79	15	empty

Interfaces

7 interfaces between chains.

B–E · 860 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 847 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 800 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 282 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 244 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1X1X · Water-mediate interaction at aprotein-protein interface · the same entry in another collection · chain D against D, TM-score 1.00
P11540 · AlphaFold monomer V2.0 prediction for barstar (P11540) · a predicted model of the same protein · chain F against A, TM-score 0.99

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 P00648
Every structure of UniProt P11540
Elsewhere: RCSB PDB 1X1X · PDBe 1X1X · UniProt P00648 · UniProt P11540

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