MolNFT v1 · #89803 · protein

Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism

4E05: “Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism”. X-ray diffraction, 2 ligands (NAG, NA), 3 pockets (best druggability 0.42). MolNFT v1 #89803 on GenesisL1: 3D structure, binding sites…

PDB: 4E05
Type: protein
Length: 312 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thrombin; Salivary anti-thrombin peptide anophelin
EC: 3.4.21.5
UniProt: P00734, Q9NJS1
Ligands: NAG, NA
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Thrombin (EC 3.4.21.5)	protein	29	41% helix, 0% strand	P00734
H	Thrombin (EC 3.4.21.5)	protein	253	15% helix, 35% strand	P00734
I	Salivary anti-thrombin peptide anophelin	protein	30	20% helix, 7% strand	Q9NJS1

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
NA · Sodium ion · metal · chains H

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.42	0.78	14	empty
2	100	0.40	0.76	16	empty
3	68	0.32	0.75	16	empty

Interfaces

2 interfaces between chains.

H–I · 1486 Å² buried · 28 hydrogen bonds · protein-protein
L–H · 1150 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

4E05 · Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding… · the same entry in another collection · chain L against L, 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 P00734
Every structure of UniProt Q9NJS1
Elsewhere: RCSB PDB 4E05 · PDBe 4E05 · UniProt P00734 · UniProt Q9NJS1

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