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Crystal structure of S. pombe MDB1 fha domain

Analyse Crystal structure of S. pombe MDB1 fha domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4S3H
Type: protein
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MDB1
UniProt: O14079
Ligands: SO4
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 1% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MDB1	protein	88	0% helix, 55% strand	O14079
B	MDB1	protein	89	3% helix, 53% strand	O14079
C, D	MDB1	protein	90	0% helix, 53% strand	O14079

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	319	0.69	0.83	54	empty
2	113	0.38	0.75	22	empty

Interfaces

5 interfaces between chains.

A–B · 802 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 757 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 266 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 48 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4S3H · Crystal structure of S. pombe Mdb1 FHA domain · the same entry in another collection · chain A against A, TM-score 1.00
O14079 · AlphaFold monomer V2.0 prediction for DNA damage response protein MDB1 (O14079) · a predicted model of the same protein · chain A against A, TM-score 0.70

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 O14079
Elsewhere: RCSB PDB 4S3H · PDBe 4S3H · UniProt O14079

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