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Crystal structure of an AF10 fragment

Analyse Crystal structure of an AF10 fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CKO
Type: protein
Length: 233 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein af-10; Histone-lysine N-methyltransferase, H3 lysine-79 specific
EC: 2.1.1.43
UniProt: P55197, F1Q4W7
Ligands: ZN, UNX
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 3 distinct chains · 91% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein af-10	protein	66	89% helix, 0% strand	P55197
B	Protein af-10	protein	67	90% helix, 0% strand	P55197
C, D	Histone-lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43)	protein	50	96% helix, 0% strand	F1Q4W7

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, C, B, D
UNX · Unknown atom or ion · ion · 24 copies · chains A, C, B, D

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.37	0.78	10	UNX

Interfaces

6 interfaces between chains.

B–D · 1150 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 1120 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 217 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 198 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 15 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6CKO · Crystal structure of an AF10 fragment · the same entry in another collection · chain A against A, TM-score 1.00
P55197 · AlphaFold monomer V2.0 prediction for protein af-10 (P55197) · a predicted model of the same protein · chain B against A, TM-score 0.61

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 P55197
Every structure of UniProt F1Q4W7
Elsewhere: RCSB PDB 6CKO · PDBe 6CKO · UniProt P55197 · UniProt F1Q4W7

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