MolNFT v1 · #127057 · protein

Crystal structure of rosb with bound intermediate afp (8-demethyl-8- aminoriboflavin-5'-phosphate)

5MLD · Bramp domain protein: “Crystal structure of rosb with bound intermediate afp (8-demethyl-8- aminoriboflavin-5'-phosphate)”. X-ray diffraction, 1 ligand (8DP), 20 pockets (best druggability 0.82). MolNFT v1 #127057 on GenesisL1: 3D…

PDB: 5MLD
Type: protein
Length: 2,016 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bramp domain protein
UniProt: K4REZ6
Ligands: 8DP
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Bramp domain protein	protein	252	36% helix, 18% strand	K4REZ6

Ligands and binding sites

8DP · 8-demethyl-8-aminoriboflavin-5'-phosphate · ligand · 8 copies · chains A, B, D, C, E, G, H, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.82	0.89	59	8DP
2	496	0.82	0.88	69	8DP
3	896	0.81	0.84	73	empty
4	132	0.81	0.98	42	empty
5	128	0.80	0.98	38	empty

Interfaces

19 interfaces between chains.

F–H · 3519 Å² buried · 59 hydrogen bonds · protein-protein
C–D · 3487 Å² buried · 58 hydrogen bonds · protein-protein
E–G · 3454 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3424 Å² buried · 51 hydrogen bonds · protein-protein
E–F · 2606 Å² buried · 55 hydrogen bonds · protein-protein

Compared structures

5MLD · Crystal Structure of RosB with bound intermediate AFP… · the same entry in another collection · chain H against H, TM-score 1.00
K4REZ6 · AlphaFold monomer V2.0 prediction for 8-demethyl-8-aminoriboflavin-5'-phosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.86

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 K4REZ6
Elsewhere: RCSB PDB 5MLD · PDBe 5MLD · UniProt K4REZ6

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