MolNFT v1 · #26851 · protein

Water-mediate interaction at aprotein-protein interface

1X1Y · Ribonuclease: “Water-mediate interaction at aprotein-protein interface”. X-ray diffraction, 6 pockets (best druggability 0.58). MolNFT v1 #26851 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1X1Y
Type: protein
Length: 594 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: 6 · best druggability 0.58

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Ribonuclease (EC 3.1.27.-)	protein	108	22% helix, 23% strand	P00648
B	Ribonuclease (EC 3.1.27.-)	protein	110	23% helix, 23% strand	P00648
D	Barstar	protein	90	49% helix, 19% strand	P11540
E, F	Barstar	protein	89	52% helix, 17% strand	P11540

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	345	0.58	0.76	47	empty
2	381	0.57	0.75	33	empty
3	219	0.53	0.77	35	empty
4	145	0.47	0.77	27	empty
5	99	0.44	0.79	23	empty

Interfaces

7 interfaces between chains.

B–E · 781 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 774 Å² buried · 17 hydrogen bonds · protein-protein
C–F · 754 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 279 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 217 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1X1Y · Water-mediate interaction at aprotein-protein interface · the same entry in another collection · chain F against F, TM-score 1.00
P11540 · AlphaFold monomer V2.0 prediction for barstar (P11540) · a predicted model of the same protein · chain D 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 1X1Y · PDBe 1X1Y · UniProt P00648 · UniProt P11540

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