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Crystal structure of human DLP1 in complex with gmp-pcp

Analyse Crystal structure of human DLP1 in complex with gmp-pcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3W6O
Type: protein
Length: 678 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynamin-1-like protein
EC: 3.6.5.5
UniProt: O00429
Ligands: GCP, MG, CA
Pockets: 10 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dynamin-1-like protein (EC 3.6.5.5)	protein	337	43% helix, 14% strand	O00429
B	Dynamin-1-like protein (EC 3.6.5.5)	protein	341	46% helix, 14% strand	O00429

Ligands and binding sites

GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	607	0.83	0.88	86	GCP, MG
2	371	0.78	0.87	55	GCP, MG
3	94	0.47	0.81	18	empty
4	50	0.46	0.85	16	empty
5	71	0.36	0.77	12	empty

Interfaces

1 interface between chains.

A–B · 1417 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3W6O · Crystal structure of human Dlp1 in complex with GMP-PCP · the same entry in another collection · chain A against A, TM-score 1.00
O00429 · AlphaFold monomer V2.0 prediction for dynamin-1-like protein (O00429) · a predicted model of the same protein · chain B against A, TM-score 0.76

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 O00429
Elsewhere: RCSB PDB 3W6O · PDBe 3W6O · UniProt O00429

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