MolNFT v1 · #117119 · protein

Abyu L73M L139M

5DYQ · Yd repeat-containing protein: “Abyu L73M L139M”. X-ray diffraction, 6 pockets (best druggability 0.82). MolNFT v1 #117119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DYQ
Type: protein
Length: 525 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yd repeat-containing protein
UniProt: F4F7G1
Pockets: 6 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Yd repeat-containing protein	protein	131	6% helix, 64% strand	F4F7G1
C	Yd repeat-containing protein	protein	132	6% helix, 65% strand	F4F7G1

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	134	0.82	0.98	24	EPE
2	137	0.80	0.97	24	EPE
3	154	0.79	0.95	27	EPE
4	139	0.77	0.94	25	empty
5	363	0.64	0.79	46	empty

Interfaces

2 interfaces between chains.

B–C · 867 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 442 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

5DYQ · AbyU L73M L139M · the same entry in another collection · chain A against A, TM-score 1.00

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 F4F7G1
Elsewhere: RCSB PDB 5DYQ · PDBe 5DYQ · UniProt F4F7G1

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