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Crystal structure of streptomyces caespitosus sermetstatin in complex with S. caespitosus snapalysin

Analyse Crystal structure of streptomyces caespitosus sermetstatin in complex with S.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HX3
Type: protein
Length: 1,466 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Extracellular small neutral protease; Neutral proteinase inhibitor scnpi
EC: 3.4.24.77
UniProt: P56406, Q9FDS0
Ligands: ZN
Pockets: 13 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 27% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, I	Extracellular small neutral protease (EC 3.4.24.77)	protein	134	34% helix, 20% strand	P56406
B, L	Neutral proteinase inhibitor scnpi	protein	113	23% helix, 35% strand	Q9FDS0
D	Neutral proteinase inhibitor scnpi	protein	109	23% helix, 37% strand	Q9FDS0
E	Extracellular small neutral protease (EC 3.4.24.77)	protein	132	33% helix, 20% strand	P56406
F	Neutral proteinase inhibitor scnpi	protein	112	22% helix, 35% strand	Q9FDS0
G, K	Extracellular small neutral protease (EC 3.4.24.77)	protein	133	33% helix, 23% strand	P56406
H	Neutral proteinase inhibitor scnpi	protein	108	22% helix, 36% strand	Q9FDS0
J	Neutral proteinase inhibitor scnpi	protein	111	22% helix, 35% strand	Q9FDS0

Ligands and binding sites

ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
GOL · Glycerol · additive · 2 copies · chains C, D, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	916	0.72	0.77	70	empty
2	569	0.64	0.75	69	empty
3	454	0.57	0.74	50	empty
4	122	0.46	0.79	27	empty
5	88	0.45	0.81	20	empty

Interfaces

21 interfaces between chains.

G–H · 984 Å² buried · 20 hydrogen bonds · protein-protein
J–L · 951 Å² buried · 7 hydrogen bonds · protein-protein
K–L · 939 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 936 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 931 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide (disulfide).

Compared structures

4HX3 · Crystal structure of Streptomyces caespitosus sermetstatin in complex with S. caespitosus… · 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 P56406
Every structure of UniProt Q9FDS0
Elsewhere: RCSB PDB 4HX3 · PDBe 4HX3 · UniProt P56406 · UniProt Q9FDS0

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