MolNFT v1 · #152322 · protein

Crystal structure of methyladenine demethylase

6IE2 · Nucleic acid dioxygenase ALKBH1: “Crystal structure of methyladenine demethylase”. X-ray diffraction, 2 ligands (AKG, MN), 20 pockets (best druggability 0.77). MolNFT v1 #152322 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6IE2
Type: protein
Length: 2,578 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleic acid dioxygenase ALKBH1
EC: 1.14.11.51
UniProt: Q13686
Ligands: AKG, MN
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 24% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.51)	protein	321	25% helix, 23% strand	Q13686
B, C, D	Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.51)	protein	323	21% helix, 21% strand	Q13686
E	Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.51)	protein	317	25% helix, 24% strand	Q13686
F, H	Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.51)	protein	324	27% helix, 22% strand	Q13686
G	Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.51)	protein	323	24% helix, 25% strand	Q13686

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	914	0.77	0.80	70	empty
2	960	0.77	0.80	74	empty
3	870	0.73	0.77	100	empty
4	789	0.71	0.77	86	empty
5	122	0.65	0.88	27	MN, AKG

Interfaces

12 interfaces between chains.

B–F · 456 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 439 Å² buried · 9 hydrogen bonds · protein-protein
C–E · 425 Å² buried · 6 hydrogen bonds · protein-protein
C–H · 413 Å² buried · 4 hydrogen bonds · protein-protein
B–G · 407 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6IE2 · Crystal structure of methyladenine demethylase · the same entry in another collection · chain H against H, TM-score 1.00
Q13686 · AlphaFold monomer V2.0 prediction for nucleic acid dioxygenase ALKBH1 (Q13686) · a predicted model of the same protein · chain B 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 Q13686
Elsewhere: RCSB PDB 6IE2 · PDBe 6IE2 · UniProt Q13686

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