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Crystal structure of an unfused MRE11-NBS1 complex with two manganese ions per active site

Analyse Crystal structure of an unfused MRE11-NBS1 complex with two manganese ions per… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FBW
Type: protein
Length: 802 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD32; DNA repair and telomere maintenance protein NBS1
UniProt: Q09683, O43070
Ligands: MN
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 24% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair protein RAD32	protein	379	25% helix, 27% strand	Q09683
B	DNA repair protein RAD32	protein	386	24% helix, 27% strand	Q09683
C	DNA repair and telomere maintenance protein NBS1	protein	21	0% helix, 24% strand	O43070
D	DNA repair and telomere maintenance protein NBS1	protein	16	25% helix, 31% strand	O43070

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, B

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

Pockets

8 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	73	0.69	0.95	27	empty
2	60	0.68	0.96	27	empty
3	82	0.44	0.80	18	empty
4	145	0.42	0.75	25	empty
5	77	0.34	0.75	22	empty

Interfaces

4 interfaces between chains.

A–B · 1450 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1356 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 948 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 180 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4FBW · Crystal structure of an unfused Mre11-Nbs1 complex with two manganese ions per active site · the same entry in another collection · chain A against A, TM-score 1.00
Q09683 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD32 (Q09683) · a predicted model of the same protein · chain B against A, TM-score 1.00
O43070 · AlphaFold monomer V2.0 prediction for DNA repair and telomere maintenance protein NBS1… · a predicted model of the same protein · chain D against A, TM-score 0.25

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 Q09683
Every structure of UniProt O43070
Elsewhere: RCSB PDB 4FBW · PDBe 4FBW · UniProt Q09683 · UniProt O43070

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