MolNFT v1 · #173265 · protein

Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex with udp

7AUA: “Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex with udp”. Electron microscopy, 5 ligands (UDP, NAG, BMA), 20 pockets (best druggability 0.81). MolNFT v1 #173265 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7AUA
Type: protein
Length: 1,372 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exostosin-like 3
EC: 2.4.1.223
UniProt: O43909
Ligands: UDP, NAG, BMA, MAN, MN
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Exostosin-like 3 (EC 2.4.1.223)	protein	686	33% helix, 16% strand	O43909

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.81	0.83	76	empty
2	267	0.80	0.92	50	empty
3	285	0.79	0.91	52	empty
4	229	0.77	0.91	56	empty
5	257	0.76	0.89	42	empty

Interfaces

1 interface between chains.

A–B · 4702 Å² buried · 59 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

7AUA · Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex with UDP · the same entry in another collection · chain B against B, TM-score 1.00
O43909 · AlphaFold monomer V2.0 prediction for exostosin-like 3 (O43909) · a predicted model of the same protein · chain B 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 O43909
Elsewhere: RCSB PDB 7AUA · PDBe 7AUA · UniProt O43909

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