MolNFT v1 · #41132 · protein

Crystal structure of recombinant dioclea grandiflora lectin mutant E123A-H131N-K132Q complexed with 5-bromo-4-chloro-3-indolyl-a-D- mannose

2JEC · Lectin alpha chain: “Crystal structure of recombinant dioclea grandiflora lectin mutant E123A-H131N-K132Q complexed with…”. X-ray diffraction, 3 ligands (XMM, MN, CA), 6 pockets (best druggability 0.79). MolNFT v1 #41132 on…

PDB: 2JEC
Type: protein
Length: 952 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lectin alpha chain
UniProt: P08902
Ligands: XMM, MN, CA
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Lectin alpha chain	protein	238	4% helix, 45% strand	P08902

Ligands and binding sites

XMM · 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside · ligand · 4 copies · chains A, B, C, D
MN · Manganese (II) ion · metal · 8 copies · chains A, D, B, C
CA · Calcium 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	360	0.79	0.89	71	MN
2	245	0.76	0.90	56	MN
3	69	0.74	0.98	27	empty
4	71	0.71	0.96	27	empty
5	90	0.68	0.93	23	MN

Interfaces

6 interfaces between chains.

C–D · 1195 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1110 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1065 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 927 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 45 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2JEC · crystal structure of recombinant DiocleA grandiflora lectin mutant E123A-H131N-K132Q… · the same entry in another collection · chain A against A, TM-score 1.00
P08902 · AlphaFold monomer V2.0 prediction for lectin alpha chain (P08902) · 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 P08902
Elsewhere: RCSB PDB 2JEC · PDBe 2JEC · UniProt P08902

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