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Structure of the SLAIN2C-CLIPCG1 complex

Analyse Structure of the SLAIN2C-CLIPCG1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RDV
Type: protein
Length: 315 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cap-gly domain-containing linker protein 1; Slain motif-containing protein 2
UniProt: P30622, Q9P270
Ligands: NA
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cap-gly domain-containing linker protein 1	protein	70	4% helix, 43% strand	P30622
B, C	Cap-gly domain-containing linker protein 1	protein	71	4% helix, 44% strand	P30622
D	Cap-gly domain-containing linker protein 1	protein	72	4% helix, 43% strand	P30622
E, F, H	Slain motif-containing protein 2	protein	8	38% helix, 0% strand	Q9P270
G	Slain motif-containing protein 2	protein	7	0% helix, 0% strand	Q9P270

Ligands and binding sites

NA · Sodium ion · metal · chains A, B
BME · Beta-mercaptoethanol · additive · chains C

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

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	187	0.55	0.79	45	NA
2	175	0.48	0.76	20	empty

Interfaces

11 interfaces between chains.

B–F · 466 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 462 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 456 Å² buried · 6 hydrogen bonds · protein-protein
C–G · 453 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 288 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3RDV · Structure of the SLAIN2c-CLIPCG1 complex · the same entry in another collection · chain H against H, TM-score 1.00
P30622 · AlphaFold monomer V2.0 prediction for cap-gly domain-containing linker protein 1 (P30622) · a predicted model of the same protein · chain A 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 P30622
Every structure of UniProt Q9P270
Elsewhere: RCSB PDB 3RDV · PDBe 3RDV · UniProt P30622 · UniProt Q9P270

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