MolNFT v1 · #114821 · protein

Myotubularin-related proetin 1

5C16 · Myotubularin-related protein 1: “Myotubularin-related proetin 1”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.77). MolNFT v1 #114821 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C16
Type: protein
Length: 1,948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Myotubularin-related protein 1
EC: 3.1.3.64
UniProt: Q13613
Ligands: PO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Myotubularin-related protein 1 (EC 3.1.3.64)	protein	487	41% helix, 18% strand	Q13613

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.77	0.79	84	empty
2	869	0.77	0.80	72	empty
3	447	0.72	0.82	38	empty
4	303	0.70	0.84	30	empty
5	287	0.70	0.84	28	empty

Interfaces

4 interfaces between chains.

B–C · 1030 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1022 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 356 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 245 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5C16 · Myotubularin-related proetin 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q13613 · AlphaFold monomer V2.0 prediction for myotubularin-related protein 1 (Q13613) · a predicted model of the same protein · chain A 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 Q13613
Elsewhere: RCSB PDB 5C16 · PDBe 5C16 · UniProt Q13613

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