MolNFT v1 · #12960 · protein

Rat mannose protein a (H189V I207V) complexed with man-A13-man

1KX0 · Mannose-binding protein a: “Rat mannose protein a (H189V I207V) complexed with man-A13-man”. X-ray diffraction, 3 ligands (MAN, CA, CL), 4 pockets (best druggability 0.68). MolNFT v1 #12960 on GenesisL1: 3D structure, binding sites…

PDB: 1KX0
Type: protein
Length: 447 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannose-binding protein a
UniProt: P19999
Ligands: MAN, CA, CL
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Mannose-binding protein a	protein	149	34% helix, 24% strand	P19999

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B, C
CA · Calcium ion · metal · 9 copies · chains A, B, C
CL · Chloride ion · ion · 3 copies · chains A, B, C

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	683	0.68	0.76	63	empty
2	277	0.57	0.77	32	empty
3	233	0.53	0.76	26	empty
4	213	0.52	0.76	29	empty

Interfaces

3 interfaces between chains.

A–B · 1112 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1073 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1049 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1KX0 · Rat mannose protein A (H189V I207V) complexed with man-a13-man · the same entry in another collection · chain A against A, TM-score 1.00
P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P19999
Elsewhere: RCSB PDB 1KX0 · PDBe 1KX0 · UniProt P19999

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