MolNFT v1 · #12961 · protein

Rat mannose protein a complexed with MAN6-GLCNAC2-asn

1KX1 · Mannose-binding protein a: “Rat mannose protein a complexed with MAN6-GLCNAC2-asn”. X-ray diffraction, 2 ligands (MAN, CA), 9 pockets (best druggability 0.69). MolNFT v1 #12961 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1KX1
Type: protein
Length: 894 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannose-binding protein a
UniProt: P19999
Ligands: MAN, CA
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Mannose-binding protein a	protein	149	36% helix, 28% strand	P19999

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 14 copies · chains C, F, B, E
CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F

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

Pockets

9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	745	0.69	0.76	65	empty
2	600	0.66	0.76	54	empty
3	294	0.55	0.75	34	empty
4	225	0.54	0.77	26	empty
5	263	0.52	0.75	31	empty

Interfaces

7 interfaces between chains.

E–F · 1079 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 1065 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1055 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1047 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1046 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

1KX1 · Rat mannose protein A complexed with Man6-GlcNAc2-Asn · the same entry in another collection · chain F against F, 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 0.98

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 1KX1 · PDBe 1KX1 · UniProt P19999

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