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Crystal structure of septin 2 in complex with gppnhp and MG2+

Analyse Crystal structure of septin 2 in complex with gppnhp and MG2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FTQ
Type: protein
Length: 999 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Septin-2
UniProt: P42208
Ligands: GNP, MG
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Septin-2	protein	254	40% helix, 22% strand	P42208
B	Septin-2	protein	252	40% helix, 21% strand	P42208
C	Septin-2	protein	250	38% helix, 23% strand	P42208
D	Septin-2	protein	243	41% helix, 23% strand	P42208

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	536	0.76	0.84	50	MG, GNP
2	534	0.75	0.83	50	MG, GNP
3	671	0.75	0.81	73	MG, GNP
4	440	0.72	0.82	48	MG, GNP
5	1061	0.72	0.75	79	empty

Interfaces

3 interfaces between chains.

A–B · 1350 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 1176 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 339 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3FTQ · Crystal structure of Septin 2 in complex with GppNHp and Mg2+ · the same entry in another collection · chain D against D, TM-score 1.00
P42208 · AlphaFold monomer V2.0 prediction for septin-2 (P42208) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P42208
Elsewhere: RCSB PDB 3FTQ · PDBe 3FTQ · UniProt P42208

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