MolNFT v1 · #36437 · protein + DNA

Mutm crosslinked to undamaged DNA sampling A:T base pair IC1

2F5N · 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Mutm crosslinked to undamaged DNA sampling A:T base pair IC1”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.66). MolNFT v1 #36437 on GenesisL1: 3D…

PDB: 2F5N
Type: protein + DNA
Length: 279 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'…
EC: 3.2.2.23
UniProt: P84131
Ligands: ZN
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(APGPGPTPAPGPAPCPCPTPGPGPAPCPGPC)-3'	dna	14	—	—
C	5'-D(TPGPCGPTPCPCPAPGPGPTPCPTPAPCPC)-3'	dna	13	—	—
A	Formamidopyrimidine-DNA glycosidase (EC 3.2.2.23)	protein	252	31% helix, 26% strand	P84131

Ligands and binding sites

ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A

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

Pockets

3 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	470	0.66	0.78	37	empty
2	107	0.43	0.78	23	empty
3	95	0.32	0.73	16	empty

Interfaces

3 interfaces between chains.

B–C · 585 Å² buried · 60 hydrogen bonds · nucleic-nucleic
C–A · 582 Å² buried · 7 hydrogen bonds · protein-nucleic
B–A · 414 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

2F5N · MutM crosslinked to undamaged DNA sampling A:T base pair IC1 · the same entry in another collection · chain B against B, 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 P84131
Elsewhere: RCSB PDB 2F5N · PDBe 2F5N · UniProt P84131

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