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Crystal structure of apo mvl

Analyse Crystal structure of apo mvl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZHQ
Type: protein
Length: 904 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mannan-binding lectin
UniProt: Q9RHG4
Ligands: PO4
Pockets: 9 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Mannan-binding lectin	protein	113	24% helix, 50% strand	Q9RHG4

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains A, B, E, D, F
EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, E, C, D, F, G, H

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1038	0.83	0.84	108	EDO
2	232	0.75	0.89	48	EDO
3	301	0.74	0.87	57	EDO
4	372	0.73	0.84	64	EDO
5	580	0.65	0.76	45	empty

Interfaces

11 interfaces between chains.

G–H · 1998 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1995 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1960 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1946 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 424 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1ZHQ · Crystal structure of apo MVL · the same entry in another collection · chain H against H, TM-score 1.00
Q9RHG4 · AlphaFold monomer V2.0 prediction for lectin mvl (Q9RHG4) · a predicted model of the same protein · chain A against A, TM-score 0.55

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 Q9RHG4
Elsewhere: RCSB PDB 1ZHQ · PDBe 1ZHQ · UniProt Q9RHG4

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