MolNFT v1 · #152526 · protein

Crystal structure of spue-spermidine in complex with SCFV5

6IKM · Polyamine transport protein: “Crystal structure of spue-spermidine in complex with SCFV5”. X-ray diffraction, 2 ligands (SPD, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #152526 on GenesisL1: 3D structure, binding sites and…

PDB: 6IKM
Type: protein
Length: 10,080 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyamine transport protein; SCFV5
UniProt: A0A069QID4
Ligands: SPD, SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	Polyamine transport protein	protein	335	49% helix, 18% strand	A0A069QID4
a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r	SCFV5	protein	225	3% helix, 50% strand	—

Ligands and binding sites

SPD · Spermidine · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
SO4 · Sulfate ion · ion · 54 copies · chains A, K, B, G, C, I, D, J, E, H, F, M, L, R, N, O

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	937	0.86	0.88	83	empty
2	1024	0.86	0.87	92	empty
3	1008	0.85	0.86	87	empty
4	1109	0.85	0.86	103	empty
5	1101	0.85	0.86	84	empty

Interfaces

56 interfaces between chains.

Q–q · 976 Å² buried · 18 hydrogen bonds · protein-protein
E–e · 943 Å² buried · 15 hydrogen bonds · protein-protein
N–n · 941 Å² buried · 15 hydrogen bonds · protein-protein
L–l · 934 Å² buried · 13 hydrogen bonds · protein-protein
O–o · 934 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 37 disulfide, 9 covalent (disulfide, covalent ligand).

Compared structures

6IKM · Crystal structure of SpuE-Spermidine in complex with ScFv5 · the same entry in another collection · chain a against a, TM-score 1.00

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 A0A069QID4
Elsewhere: RCSB PDB 6IKM · PDBe 6IKM · UniProt A0A069QID4

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.