MolNFT v1 · #145523 · protein

Crystal structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, RIM1 (FORM2)

6CQM · Single-stranded DNA-binding protein RIM1, mitochondrial: “Crystal structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, RIM1 (FORM2)”. X-ray diffraction, 7 pockets (best druggability 0.78). MolNFT v1…

PDB: 6CQM
Type: protein
Length: 750 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Single-stranded DNA-binding protein RIM1, mitochondrial
UniProt: P32445
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 8 distinct chains · 10% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	96	10% helix, 56% strand	P32445
B	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	93	10% helix, 60% strand	P32445
C	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	96	10% helix, 60% strand	P32445
D	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	99	10% helix, 61% strand	P32445
E	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	94	10% helix, 53% strand	P32445
F	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	96	10% helix, 58% strand	P32445
G	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	90	11% helix, 58% strand	P32445
H	Single-stranded DNA-binding protein RIM1, mitochondrial	protein	86	12% helix, 53% strand	P32445

Pockets

7 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	1049	0.78	0.80	121	empty
2	247	0.56	0.77	37	empty
3	149	0.48	0.78	23	empty
4	182	0.46	0.75	23	empty
5	80	0.34	0.75	17	empty

Interfaces

15 interfaces between chains.

B–F · 1287 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1150 Å² buried · 25 hydrogen bonds · protein-protein
A–G · 1119 Å² buried · 29 hydrogen bonds · protein-protein
D–F · 508 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 363 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6CQM · Crystal Structure of mitochondrial single-stranded DNA binding proteins from S.… · the same entry in another collection · chain H against H, TM-score 1.00
P32445 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein RIM1… · a predicted model of the same protein · chain H against A, TM-score 0.97

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 P32445
Elsewhere: RCSB PDB 6CQM · PDBe 6CQM · UniProt P32445

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