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Crystal structure of hd-ptp phosphatase in complex with UBAP1

Analyse Crystal structure of hd-ptp phosphatase in complex with UBAP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LM1
Type: protein
Length: 349 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein phosphatase non-receptor type 23; Ubap-1
EC: 3.1.3.48
UniProt: Q9H3S7
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 87% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein phosphatase non-receptor type 23 (EC 3.1.3.48)	protein	339	88% helix, 0% strand	Q9H3S7
B	Ubap-1	protein	10	30% helix, 0% strand	—

Pockets

2 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	70	0.51	0.85	16	empty
2	94	0.38	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 623 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5LM1 · Crystal Structure of HD-PTP phosphatase in complex with UBAP1 · the same entry in another collection · chain B against B, TM-score 1.00
Q9H3S7 · AlphaFold monomer V2.0 prediction for tyrosine-protein phosphatase non-receptor type 23… · a predicted model of the same protein · chain A against A, TM-score 0.90

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 Q9H3S7
Elsewhere: RCSB PDB 5LM1 · PDBe 5LM1 · UniProt Q9H3S7

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