MolNFT v1 · #88120 · protein

Crystal structure of YBR137W protein

4CLC · UPF0303 protein YBR137W: “Crystal structure of YBR137W protein”. X-ray diffraction, 6 pockets (best druggability 0.70). MolNFT v1 #88120 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CLC
Type: protein
Length: 856 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0303 protein YBR137W
UniProt: P38276
Pockets: 6 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 44% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UPF0303 protein YBR137W	protein	169	45% helix, 15% strand	P38276
B	UPF0303 protein YBR137W	protein	170	42% helix, 18% strand	P38276
C	UPF0303 protein YBR137W	protein	173	43% helix, 15% strand	P38276
D	UPF0303 protein YBR137W	protein	172	44% helix, 15% strand	P38276
E	UPF0303 protein YBR137W	protein	172	46% helix, 15% strand	P38276

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.70	0.80	66	empty
2	484	0.69	0.80	56	empty
3	515	0.69	0.79	51	empty
4	771	0.67	0.75	74	empty
5	58	0.29	0.75	18	empty

Interfaces

7 interfaces between chains.

A–B · 981 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 946 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 675 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 671 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 466 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4CLC · Crystal structure of Ybr137w protein · the same entry in another collection · chain E against E, TM-score 1.00
P38276 · AlphaFold monomer V2.0 prediction for UPF0303 protein YBR137W (P38276) · 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 P38276
Elsewhere: RCSB PDB 4CLC · PDBe 4CLC · UniProt P38276

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