MolNFT v1 · #90910 · protein

The structure of ddrb from deinococcus: a new fold for single-stranded DNA binding proteins.

4EXW · Single-stranded DNA-binding protein ddrb: “The structure of ddrb from deinococcus: a new fold for single-stranded DNA binding proteins.”. X-ray diffraction, 12 pockets (best druggability 0.77). MolNFT v1 #90910 on GenesisL1: 3D…

PDB: 4EXW
Type: protein
Length: 603 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein ddrb
UniProt: Q1J1N6
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein ddrb	protein	130	17% helix, 37% strand	Q1J1N6
B	Single-stranded DNA-binding protein ddrb	protein	117	19% helix, 31% strand	Q1J1N6
C	Single-stranded DNA-binding protein ddrb	protein	124	18% helix, 37% strand	Q1J1N6
D	Single-stranded DNA-binding protein ddrb	protein	115	19% helix, 35% strand	Q1J1N6
E	Single-stranded DNA-binding protein ddrb	protein	117	19% helix, 37% strand	Q1J1N6

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	695	0.77	0.82	48	empty
2	665	0.68	0.77	76	empty
3	533	0.64	0.76	63	empty
4	464	0.63	0.76	56	empty
5	546	0.61	0.74	55	empty

Interfaces

5 interfaces between chains.

A–B · 784 Å² buried · 9 hydrogen bonds · protein-protein
A–E · 753 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 706 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 691 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 679 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 modified (engineered).

Compared structures

4EXW · The structure of DdrB from Deinococcus: a new fold for single-stranded DNA binding… · the same entry in another collection · chain E against E, TM-score 1.00
Q1J1N6 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein ddrb (Q1J1N6) · a predicted model of the same protein · chain D against A, TM-score 0.96

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 Q1J1N6
Elsewhere: RCSB PDB 4EXW · PDBe 4EXW · UniProt Q1J1N6

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