MolNFT v1 · #137347 · protein

Structure of the TTLL3 glycylase

5VLQ · LOC100158544 protein: “Structure of the TTLL3 glycylase”. X-ray diffraction, 2 ligands (ANP, SO4), 9 pockets (best druggability 0.61). MolNFT v1 #137347 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VLQ
Type: protein
Length: 804 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: LOC100158544 protein
UniProt: B2GUB3
Ligands: ANP, SO4
Pockets: 9 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	LOC100158544 protein	protein	391	44% helix, 19% strand	B2GUB3
B	LOC100158544 protein	protein	413	45% helix, 19% strand	B2GUB3

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

9 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	298	0.61	0.79	42	empty
2	189	0.52	0.78	35	empty
3	220	0.51	0.76	27	empty
4	142	0.42	0.75	24	ANP
5	129	0.41	0.75	19	empty

Interfaces

1 interface between chains.

A–B · 468 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

5VLQ · Structure of the TTLL3 Glycylase · 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 B2GUB3
Elsewhere: RCSB PDB 5VLQ · PDBe 5VLQ · UniProt B2GUB3

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