MolNFT v1 · #95639 · protein

Crystal structure of the serine protease domain of masp-3 in complex with ecotin

4IW4: “Crystal structure of the serine protease domain of masp-3 in complex with ecotin”. X-ray diffraction, 6 pockets (best druggability 0.86). MolNFT v1 #95639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4IW4
Type: protein
Length: 755 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ecotin; Mannan-binding lectin serine protease 3
UniProt: P23827, P48740
Pockets: 6 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 8% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Ecotin	protein	137	2% helix, 53% strand	P23827
D	Ecotin	protein	134	7% helix, 51% strand	P23827
E	Mannan-binding lectin serine protease 3	protein	244	11% helix, 34% strand	P48740
F	Mannan-binding lectin serine protease 3	protein	240	10% helix, 34% strand	P48740

Pockets

6 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	924	0.86	0.88	116	empty
2	152	0.69	0.89	20	empty
3	172	0.45	0.75	26	empty
4	69	0.31	0.74	12	empty
5	62	0.28	0.73	15	empty

Interfaces

5 interfaces between chains.

C–D · 1648 Å² buried · 34 hydrogen bonds · protein-protein
D–F · 1326 Å² buried · 20 hydrogen bonds · protein-protein
C–E · 1238 Å² buried · 18 hydrogen bonds · protein-protein
C–F · 731 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 670 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4IW4 · Crystal structure of the serine protease domain of MASP-3 in complex with ecotin · the same entry in another collection · chain F against F, TM-score 1.00
P23827 · AlphaFold monomer V2.0 prediction for ecotin (P23827) · a predicted model of the same protein · chain D against A, TM-score 0.98
P48740 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 1 (P48740) · a predicted model of the same protein · chain F against A, TM-score 0.89

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 P23827
Every structure of UniProt P48740
Elsewhere: RCSB PDB 4IW4 · PDBe 4IW4 · UniProt P23827 · UniProt P48740

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