MolNFT v1 · #141381 · protein

Crystal structure of cona-R5M

5Z5L · Concanavalin-a: “Crystal structure of cona-R5M”. X-ray diffraction, 3 ligands (96O, MN, CA), 6 pockets (best druggability 0.79). MolNFT v1 #141381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Z5L
Type: protein
Length: 919 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: 96O, MN, CA
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Concanavalin-a	protein	233	6% helix, 43% strand	P02866
B	Concanavalin-a	protein	227	5% helix, 45% strand	P02866
C	Concanavalin-a	protein	229	4% helix, 45% strand	P02866
D	Concanavalin-a	protein	230	4% helix, 42% strand	P02866

Ligands and binding sites

96O · (1-methyl-1H-1,2,3-triazol-4-yl)methyl alpha-D-mannopyranoside · ligand · chains B
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	666	0.79	0.84	81	empty
2	351	0.75	0.86	43	empty
3	83	0.63	0.91	23	MN, CA
4	53	0.60	0.93	18	MN, CA
5	89	0.45	0.80	21	empty

Interfaces

4 interfaces between chains.

A–B · 1104 Å² buried · 20 hydrogen bonds · protein-protein
C–D · 1007 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 596 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 495 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5Z5L · Crystal structure of ConA-R5M · the same entry in another collection · chain D against D, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain B against A, TM-score 0.51

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 P02866
Elsewhere: RCSB PDB 5Z5L · PDBe 5Z5L · UniProt P02866

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