MolNFT v1 · #126910 · protein

Crystal structure of a DM9 domain containing protein from crassostrea gigas with D22A mutation

5MH2 · Natterin-3: “Crystal structure of a DM9 domain containing protein from crassostrea gigas with D22A mutation”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.83). MolNFT v1 #126910 on GenesisL1: 3D structure…

PDB: 5MH2
Type: protein
Length: 572 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Natterin-3
UniProt: K1QRB6
Ligands: CL
Pockets: 7 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 62% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Natterin-3	protein	143	0% helix, 62% strand	K1QRB6

Ligands and binding sites

CL · Chloride ion · ion · 2 copies · chains A, C
GOL · Glycerol · additive · chains B

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

Pockets

7 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	207	0.83	0.97	27	empty
2	199	0.83	0.97	27	empty
3	351	0.64	0.79	46	empty
4	61	0.29	0.74	18	empty
5	52	0.27	0.74	14	empty

Interfaces

3 interfaces between chains.

C–D · 1209 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1201 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 302 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5MH2 · Crystal structure of a DM9 domain containing protein from Crassostrea gigas with D22A… · 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 K1QRB6
Elsewhere: RCSB PDB 5MH2 · PDBe 5MH2 · UniProt K1QRB6

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