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Crystal structure of P97/VCP N in complex with OTU1 ubxl

Analyse Crystal structure of P97/VCP N in complex with OTU1 ubxl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KDI
Type: protein
Length: 463 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transitional endoplasmic reticulum ATPase; Ubiquitin thioesterase OTU1
EC: 3.6.4.6, 3.4.19.12
UniProt: P55072, P43558
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	157	15% helix, 41% strand	P55072
B	Transitional endoplasmic reticulum ATPase (EC 3.6.4.6)	protein	166	13% helix, 43% strand	P55072
C	Ubiquitin thioesterase OTU1 (EC 3.4.19.12)	protein	65	17% helix, 38% strand	P43558
D	Ubiquitin thioesterase OTU1 (EC 3.4.19.12)	protein	75	19% helix, 41% strand	P43558

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	207	0.65	0.84	37	empty
2	164	0.60	0.83	30	empty
3	137	0.43	0.76	22	empty

Interfaces

3 interfaces between chains.

B–D · 654 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 652 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 645 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4KDI · Crystal structure of p97/VCP N in complex with OTU1 UBXL · the same entry in another collection · chain D against D, TM-score 1.00
P43558 · AlphaFold monomer V2.0 prediction for ubiquitin thioesterase OTU1 (P43558) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P55072
Every structure of UniProt P43558
Elsewhere: RCSB PDB 4KDI · PDBe 4KDI · UniProt P55072 · UniProt P43558

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