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Crystal structure of the dynamin 3 GTPase domain bound with GDP

Analyse Crystal structure of the dynamin 3 GTPase domain bound with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L43
Type: protein
Length: 965 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynamin-3
EC: 3.6.5.5
UniProt: Q9UQ16
Ligands: GDP, UNX
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dynamin-3 (EC 3.6.5.5)	protein	242	37% helix, 19% strand	Q9UQ16
B	Dynamin-3 (EC 3.6.5.5)	protein	246	38% helix, 20% strand	Q9UQ16
C	Dynamin-3 (EC 3.6.5.5)	protein	238	36% helix, 19% strand	Q9UQ16
D	Dynamin-3 (EC 3.6.5.5)	protein	239	37% helix, 20% strand	Q9UQ16

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
UNX · Unknown atom or ion · ion · 6 copies · chains A, B, C, D

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	902	0.83	0.85	110	GDP, UNX
2	1192	0.83	0.84	119	GDP, UNX
3	109	0.51	0.82	27	empty
4	79	0.41	0.79	22	empty
5	68	0.40	0.79	15	empty

Interfaces

4 interfaces between chains.

A–D · 1341 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1306 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 444 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 435 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3L43 · Crystal structure of the dynamin 3 GTPase domain bound with GDP · the same entry in another collection · chain D against D, TM-score 1.00
Q9UQ16 · AlphaFold monomer V2.0 prediction for dynamin-3 (Q9UQ16) · a predicted model of the same protein · chain C 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 Q9UQ16
Elsewhere: RCSB PDB 3L43 · PDBe 3L43 · UniProt Q9UQ16

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