MolNFT v1 · #68569 · protein

The crystal structure of MDC1 brct T2067D in complex with a minimal recognition tetrapeptide with an amidated C-terminus

3K05 · Mediator of DNA damage checkpoint protein 1: “The crystal structure of MDC1 brct T2067D in complex with a minimal recognition tetrapeptide with an amidated…”. X-ray diffraction, 1 ligand (NH2), 2 pockets (best druggability 0.61).…

PDB: 3K05
Type: protein
Length: 401 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mediator of DNA damage checkpoint protein 1; Phospho peptide
UniProt: Q14676
Ligands: NH2
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mediator of DNA damage checkpoint protein 1	protein	193	45% helix, 14% strand	Q14676
B	Mediator of DNA damage checkpoint protein 1	protein	200	43% helix, 15% strand	Q14676
C, D	Phospho peptide	protein	4	0% helix, 25% strand	—

Ligands and binding sites

NH2 · Amino group · ion · 2 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 copies · chains A, B, C, D

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	386	0.61	0.77	50	NH2, GOL
2	221	0.47	0.74	35	NH2

Interfaces

6 interfaces between chains.

B–D · 373 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 357 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 350 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 171 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 130 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

3K05 · The crystal structure of MDC1 BRCT T2067D in complex with a minimal recognition… · the same entry in another collection · chain A against A, TM-score 1.00
Q14676 · AlphaFold monomer V2.0 prediction for mediator of DNA damage checkpoint protein 1 (Q14676) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q14676
Elsewhere: RCSB PDB 3K05 · PDBe 3K05 · UniProt Q14676

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