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Human CD38 in complex with nanobody MU1053

Analyse Human CD38 in complex with nanobody MU1053 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5F1K
Type: protein
Length: 727 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1; Nanobody MU1053
EC: 3.2.2.6
UniProt: P28907
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6)	protein	244	45% helix, 14% strand	P28907
B	ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6)	protein	237	46% helix, 14% strand	P28907
C, D	Nanobody MU1053	protein	123	5% helix, 48% strand	—

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.78	0.80	122	empty
2	275	0.64	0.81	29	empty
3	282	0.64	0.81	34	empty
4	333	0.60	0.77	40	empty
5	351	0.60	0.77	41	empty

Interfaces

5 interfaces between chains.

A–C · 898 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 786 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 625 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 301 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 289 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

Compared structures

5F1K · human CD38 in complex with nanobody MU1053 · 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 0.99

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 P28907
Elsewhere: RCSB PDB 5F1K · PDBe 5F1K · UniProt P28907

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