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Crystal structure of an Fab fragment in complex with a peptide from bacillus subtilis RNase Y

Analyse Crystal structure of an Fab fragment in complex with a peptide from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F7T
Type: protein
Length: 881 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab RY79-90, light chain; Fab RY79-90, heavy chain; Ribonuclease Y
EC: 3.1.-.-
UniProt: O31774
Ligands: MG
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 3% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab RY79-90, light chain	protein	217	3% helix, 54% strand	—
B, H	Fab RY79-90, heavy chain	protein	211	4% helix, 52% strand	—
C, D	Ribonuclease Y (EC 3.1.-.-)	protein	12	0% helix, 8% strand	O31774
L	Fab RY79-90, light chain	protein	218	3% helix, 54% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · chains L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1058	0.73	0.76	119	empty
2	172	0.47	0.76	20	empty
3	80	0.45	0.81	16	empty
4	156	0.41	0.73	20	empty
5	117	0.40	0.76	21	empty

Interfaces

9 interfaces between chains.

H–L · 1760 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1719 Å² buried · 6 hydrogen bonds · protein-protein
C–L · 505 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 474 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 439 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6F7T · Crystal Structure of an Fab fragment in complex with a peptide from Bacillus subtilis… · the same entry in another collection · chain C against C, TM-score 1.00
O31774 · AlphaFold monomer V2.0 prediction for ribonuclease Y (O31774) · a predicted model of the same protein · chain C against A, TM-score 0.31

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 O31774
Elsewhere: RCSB PDB 6F7T · PDBe 6F7T · UniProt O31774

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