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Structure of CSM1 C-terminal domain, P21212 form

Analyse Structure of CSM1 C-terminal domain, P21212 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N4S
Type: protein
Length: 398 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monopolin complex subunit CSM1
UniProt: P25651
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Monopolin complex subunit CSM1	protein	98	40% helix, 34% strand	P25651
B	Monopolin complex subunit CSM1	protein	102	39% helix, 31% strand	P25651
C	Monopolin complex subunit CSM1	protein	98	42% helix, 35% strand	P25651
D	Monopolin complex subunit CSM1	protein	100	40% helix, 32% strand	P25651

Ligands and binding sites

1PE · Pentaethylene glycol · additive · 10 copies · chains B, A, D, C

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

Pockets

5 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	322	0.64	0.80	31	empty
2	120	0.42	0.76	16	1PE
3	51	0.34	0.78	11	1PE
4	71	0.33	0.75	16	empty
5	52	0.27	0.74	11	1PE

Interfaces

4 interfaces between chains.

C–D · 1260 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 1195 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 271 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 190 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3N4S · Structure of Csm1 C-terminal domain, P21212 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 A 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 3N4S · PDBe 3N4S · UniProt P25651

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