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Crystal structure of RIB7 mutant D33N from methanosarcina mazei

Analyse Crystal structure of RIB7 mutant D33N from methanosarcina mazei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XV0
Type: protein
Length: 1,371 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Conserved protein
UniProt: Q8PYN5
Ligands: NAP
Pockets: 15 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Conserved protein	protein	238	26% helix, 27% strand	Q8PYN5
B, C	Conserved protein	protein	224	27% helix, 29% strand	Q8PYN5
D, E	Conserved protein	protein	223	28% helix, 26% strand	Q8PYN5
F	Conserved protein	protein	239	26% helix, 27% strand	Q8PYN5

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

15 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	554	0.73	0.81	53	NAP
2	549	0.73	0.81	53	NAP
3	502	0.72	0.81	50	NAP
4	555	0.72	0.81	50	NAP
5	507	0.72	0.81	56	NAP

Interfaces

5 interfaces between chains.

C–D · 1888 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1880 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1856 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 774 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 767 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5XV0 · Crystal structure of Rib7 mutant D33N from Methanosarcina mazei · the same entry in another collection · chain A against A, 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 Q8PYN5
Elsewhere: RCSB PDB 5XV0 · PDBe 5XV0 · UniProt Q8PYN5

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