MolNFT v1 · #72309 · protein

Structure of CSM1 C-terminal domain, R3 form

3N4R · Monopolin complex subunit CSM1: “Structure of CSM1 C-terminal domain, R3 form”. X-ray diffraction, 3 pockets (best druggability 0.67). MolNFT v1 #72309 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3N4R
Type: protein
Length: 382 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monopolin complex subunit CSM1
UniProt: P25651
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Monopolin complex subunit CSM1	protein	93	41% helix, 30% strand	P25651
B	Monopolin complex subunit CSM1	protein	98	39% helix, 33% strand	P25651
C	Monopolin complex subunit CSM1	protein	98	43% helix, 37% strand	P25651
D	Monopolin complex subunit CSM1	protein	93	48% helix, 29% strand	P25651

Ligands and binding sites

1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D
MLI · Malonate ion · additive · 3 copies · chains A, B, C

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

Pockets

3 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	450	0.67	0.79	35	1PE
2	78	0.41	0.80	28	1PE
3	50	0.31	0.75	10	1PE

Interfaces

3 interfaces between chains.

C–D · 1187 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1169 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 759 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

3N4R · Structure of Csm1 C-terminal domain, R3 form · the same entry in another collection · chain D against D, TM-score 1.00
P25651 · AlphaFold monomer V2.0 prediction for monopolin complex subunit CSM1 (P25651) · a predicted model of the same protein · chain B 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 P25651
Elsewhere: RCSB PDB 3N4R · PDBe 3N4R · UniProt P25651

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