MolNFT v1 · #127302 · protein

Structure of the DCC1 protein

5MSN: “Structure of the DCC1 protein”. X-ray diffraction, 18 pockets (best druggability 0.80). MolNFT v1 #127302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MSN
Type: protein
Length: 1,025 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DCC1 protein
UniProt: P25559
Pockets: 18 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DCC1 protein	protein	259	46% helix, 14% strand	P25559
B	DCC1 protein	protein	256	46% helix, 16% strand	P25559
C	DCC1 protein	protein	255	47% helix, 15% strand	P25559
D	DCC1 protein	protein	255	46% helix, 16% strand	P25559

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	703	0.80	0.84	91	empty
2	896	0.79	0.82	83	empty
3	601	0.79	0.84	58	empty
4	455	0.71	0.82	42	empty
5	173	0.64	0.85	22	empty

Interfaces

4 interfaces between chains.

A–B · 1957 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1817 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 381 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 42 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5MSN · Structure of the Dcc1 Protein · the same entry in another collection · chain D against D, TM-score 1.00
P25559 · AlphaFold monomer V2.0 prediction for sister chromatid cohesion protein DCC1 (P25559) · a predicted model of the same protein · chain D 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 P25559
Elsewhere: RCSB PDB 5MSN · PDBe 5MSN · UniProt P25559

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