MolNFT v1 · #34057 · protein

Cratylia folibunda seed lectin at acidic pH

2D3R · Lectin alpha chain: “Cratylia folibunda seed lectin at acidic pH”. X-ray diffraction, 2 ligands (CA, MN), 6 pockets (best druggability 0.87). MolNFT v1 #34057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D3R
Type: protein
Length: 944 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin alpha chain
UniProt: P81517
Ligands: CA, MN
Pockets: 6 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Lectin alpha chain	protein	236	3% helix, 46% strand	P81517

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.87	0.88	123	empty
2	85	0.48	0.82	20	empty
3	93	0.43	0.79	18	empty
4	177	0.41	0.73	33	empty
5	97	0.32	0.73	22	empty

Interfaces

6 interfaces between chains.

C–D · 1142 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1138 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1062 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 1034 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 33 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2D3R · Cratylia folibunda seed lectin at acidic pH · the same entry in another collection · chain A against A, TM-score 1.00
P81517 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P81517) · 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 P81517
Elsewhere: RCSB PDB 2D3R · PDBe 2D3R · UniProt P81517

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