MolNFT v1 · #106287 · protein

Carp fishelectin, holo form

4RUS · Fish-egg lectin: “Carp fishelectin, holo form”. X-ray diffraction, 4 ligands (NAG, NDG, CA), 13 pockets (best druggability 0.84). MolNFT v1 #106287 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RUS
Type: protein
Length: 1,419 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fish-egg lectin
UniProt: P68512
Ligands: NAG, NDG, CA, MG
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, E, F	Fish-egg lectin	protein	237	2% helix, 52% strand	P68512
B	Fish-egg lectin	protein	235	2% helix, 52% strand	P68512
C	Fish-egg lectin	protein	236	2% helix, 52% strand	P68512

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, D, B, F, C, E
NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, B, D, F
CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 4 copies · chains A, D, E, B, C, F
1PE · Pentaethylene glycol · additive · 2 copies · chains A, E

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

Pockets

13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	771	0.84	0.87	120	empty
2	130	0.79	0.97	31	empty
3	113	0.78	0.97	28	empty
4	121	0.78	0.96	28	empty
5	392	0.64	0.79	36	MG

Interfaces

12 interfaces between chains.

C–D · 1544 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 1522 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1498 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 392 Å² buried · 5 hydrogen bonds · protein-protein
A–E · 392 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4RUS · Carp Fishelectin, holo form · the same entry in another collection · chain F against F, TM-score 1.00
P68512 · AlphaFold monomer V2.0 prediction for fish-egg lectin (P68512) · a predicted model of the same protein · chain D against A, TM-score 1.00

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 P68512
Elsewhere: RCSB PDB 4RUS · PDBe 4RUS · UniProt P68512

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