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Trimeric structure of a C-type mannose-binding protein

Analyse Trimeric structure of a C-type mannose-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RTM
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: CA, CL
Pockets: 4 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1, 2, 3	Mannose-binding protein-a	protein	149	36% helix, 26% strand	P19999

Ligands and binding sites

CA · Calcium ion · metal · 9 copies · chains 1, 2, 3
CL · Chloride ion · ion · 3 copies · chains 1, 2, 3
GOL · Glycerol · additive · 15 copies · chains 1, 3, 2

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

Pockets

4 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	662	0.66	0.75	61	empty
2	232	0.55	0.77	30	GOL
3	254	0.53	0.75	28	GOL
4	169	0.47	0.75	25	GOL

Interfaces

3 interfaces between chains.

1–2 · 1087 Å² buried · 7 hydrogen bonds · protein-protein
2–3 · 1081 Å² buried · 7 hydrogen bonds · protein-protein
1–3 · 1065 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

1RTM · Trimeric structure of a C-type mannose-binding protein · the same entry in another collection · chain 2 against 2, TM-score 1.00
P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain 1 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 1RTM · PDBe 1RTM · UniProt P19999

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