MolNFT v1 · #80332 · protein

Crystal structure of apo-spud

3TTK · Polyamine transport protein: “Crystal structure of apo-spud”. X-ray diffraction, 8 pockets (best druggability 0.74). MolNFT v1 #80332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3TTK
Type: protein
Length: 1,020 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyamine transport protein
UniProt: Q9I6J1
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Polyamine transport protein	protein	340	47% helix, 17% strand	Q9I6J1

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.74	0.77	75	empty
2	986	0.73	0.77	81	empty
3	558	0.68	0.78	39	empty
4	407	0.61	0.76	45	empty
5	109	0.36	0.74	16	empty

Interfaces

2 interfaces between chains.

A–C · 464 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 404 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3TTK · Crystal structure of apo-SpuD · the same entry in another collection · chain A against A, TM-score 1.00
Q9I6J1 · AlphaFold monomer V2.0 prediction for putrescine-binding periplasmic protein spud (Q9I6J1) · a predicted model of the same protein · chain A against A, TM-score 0.78

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 Q9I6J1
Elsewhere: RCSB PDB 3TTK · PDBe 3TTK · UniProt Q9I6J1

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