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Crystal structure of the chromo domain of human MRG15

Analyse Crystal structure of the chromo domain of human MRG15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F5K
Type: protein
Length: 483 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mortality factor 4-like protein 1
UniProt: Q9UBU8
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 6 distinct chains · 29% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mortality factor 4-like protein 1	protein	83	31% helix, 39% strand	Q9UBU8
B	Mortality factor 4-like protein 1	protein	85	28% helix, 40% strand	Q9UBU8
C	Mortality factor 4-like protein 1	protein	80	30% helix, 36% strand	Q9UBU8
D	Mortality factor 4-like protein 1	protein	79	28% helix, 41% strand	Q9UBU8
E	Mortality factor 4-like protein 1	protein	78	27% helix, 38% strand	Q9UBU8
F	Mortality factor 4-like protein 1	protein	78	32% helix, 37% strand	Q9UBU8

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	997	0.80	0.81	79	empty
2	763	0.79	0.83	63	empty
3	131	0.46	0.78	19	empty
4	87	0.44	0.80	14	empty
5	96	0.38	0.76	20	empty

Interfaces

7 interfaces between chains.

A–C · 642 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 551 Å² buried · 3 hydrogen bonds · protein-protein
D–F · 522 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 517 Å² buried · 3 hydrogen bonds · protein-protein
C–E · 506 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2F5K · Crystal structure of the chromo domain of human MRG15 · the same entry in another collection · chain F against F, TM-score 1.00
Q9UBU8 · AlphaFold monomer V2.0 prediction for mortality factor 4-like protein 1 (Q9UBU8) · a predicted model of the same protein · chain E against A, TM-score 0.93

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 Q9UBU8
Elsewhere: RCSB PDB 2F5K · PDBe 2F5K · UniProt Q9UBU8

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