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Crystal structure of the HMHF1/HMHF2 histone-fold tetramer in complex with fanconi anemia associated helicase hfancm

Analyse Crystal structure of the HMHF1/HMHF2 histone-fold tetramer in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E45
Type: protein
Length: 1,334 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Centromere protein S; Centromere protein X; Fanconi anemia group M protein
EC: 3.6.4.13
UniProt: Q8N2Z9, A8MT69, Q8IYD8
Ligands: ZN
Pockets: 18 · best druggability 0.70

Structure

x-ray diffraction · 7 distinct chains · 65% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Centromere protein S	protein	102	81% helix, 4% strand	Q8N2Z9
B, D, G, I, L, N	Centromere protein X	protein	74	72% helix, 5% strand	A8MT69
C, H	Centromere protein S	protein	94	79% helix, 4% strand	Q8N2Z9
E, J	Fanconi anemia group M protein (EC 3.6.4.13)	protein	105	40% helix, 6% strand	Q8IYD8
K	Centromere protein S	protein	94	78% helix, 3% strand	Q8N2Z9
M	Centromere protein S	protein	93	76% helix, 4% strand	Q8N2Z9
O	Fanconi anemia group M protein (EC 3.6.4.13)	protein	101	37% helix, 6% strand	Q8IYD8

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains D, E, I, J, N, O
GOL · Glycerol · additive · 2 copies · chains A, B, H, J

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	219	0.70	0.87	43	empty
2	210	0.69	0.87	37	empty
3	352	0.69	0.82	49	empty
4	400	0.64	0.78	44	empty
5	267	0.60	0.79	34	empty

Interfaces

37 interfaces between chains.

C–D · 2352 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 2348 Å² buried · 14 hydrogen bonds · protein-protein
H–I · 2317 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 2310 Å² buried · 15 hydrogen bonds · protein-protein
M–N · 2272 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4E45 · Crystal structure of the hMHF1/hMHF2 Histone-Fold Tetramer in Complex with Fanconi Anemia… · the same entry in another collection · chain K against K, 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 Q8N2Z9
Every structure of UniProt A8MT69
Every structure of UniProt Q8IYD8
Elsewhere: RCSB PDB 4E45 · PDBe 4E45 · UniProt Q8N2Z9 · UniProt A8MT69 · UniProt Q8IYD8

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