MolNFT v1 · #27058 · protein

Crystal structure of E. COLI yiil protein containing L-rhamnose

1X8D · Hypothetical protein yiil: “Crystal structure of E. COLI yiil protein containing L-rhamnose”. X-ray diffraction, 1 ligand (RNS), 7 pockets (best druggability 0.69). MolNFT v1 #27058 on GenesisL1: 3D structure, binding sites and…

PDB: 1X8D
Type: protein
Length: 416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein yiil
UniProt: P32156
Ligands: RNS
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Hypothetical protein yiil	protein	104	33% helix, 35% strand	P32156

Ligands and binding sites

RNS · L-rhamnose · ligand · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.69	0.86	30	RNS
2	218	0.69	0.85	30	RNS
3	202	0.68	0.85	30	RNS
4	237	0.68	0.84	32	RNS
5	238	0.61	0.81	41	empty

Interfaces

4 interfaces between chains.

C–D · 1777 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1752 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 263 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 262 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1X8D · Crystal structure of E. coli YiiL protein containing L-rhamnose · the same entry in another collection · chain A against A, TM-score 1.00
P32156 · AlphaFold monomer V2.0 prediction for L-rhamnose mutarotase (P32156) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P32156
Elsewhere: RCSB PDB 1X8D · PDBe 1X8D · UniProt P32156

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