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Crystal structure of human CD38 extracellular domain

Analyse Crystal structure of human CD38 extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YH3
Type: protein
Length: 504 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosyl cyclase 1
EC: 3.2.2.5
UniProt: P28907
Pockets: 7 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ADP-ribosyl cyclase 1 (EC 3.2.2.5)	protein	252	43% helix, 13% strand	P28907

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.58	0.76	36	empty
2	289	0.57	0.77	40	empty
3	120	0.55	0.83	18	empty
4	98	0.53	0.83	18	empty
5	88	0.37	0.76	21	empty

Interfaces

1 interface between chains.

A–B · 741 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

1YH3 · Crystal structure of human CD38 extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P28907
Elsewhere: RCSB PDB 1YH3 · PDBe 1YH3 · UniProt P28907

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