MolNFT v1 · #111256 · protein

Crystal structure of dpgc with bound substrate analog and xe on oxygen diffusion pathway

4YLH: “Crystal structure of dpgc with bound substrate analog and xe on oxygen diffusion pathway”. X-ray diffraction, 2 ligands (YE1, XE), 20 pockets (best druggability 0.83). MolNFT v1 #111256 on GenesisL1: 3D structure, binding sites and…

PDB: 4YLH
Type: protein
Length: 5,059 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dpgc
UniProt: Q8KLK7
Ligands: YE1, XE
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 55% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, F, I, L	Dpgc	protein	421	55% helix, 12% strand	Q8KLK7
B, G, H, K	Dpgc	protein	422	56% helix, 12% strand	Q8KLK7
D	Dpgc	protein	423	55% helix, 12% strand	Q8KLK7
J	Dpgc	protein	422	55% helix, 12% strand	Q8KLK7

Ligands and binding sites

YE1 · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R)-4-({3-[(2-{[(3,5-dihydroxyphenyl)acetyl]amino}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
XE · Xenon · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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	934	0.83	0.84	99	empty
2	895	0.83	0.85	89	empty
3	812	0.82	0.85	70	empty
4	806	0.81	0.84	69	empty
5	1044	0.75	0.78	71	empty

Interfaces

21 interfaces between chains.

K–L · 1502 Å² buried · 19 hydrogen bonds · protein-protein
H–I · 1496 Å² buried · 20 hydrogen bonds · protein-protein
B–C · 1481 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1477 Å² buried · 18 hydrogen bonds · protein-protein
J–K · 1458 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4YLH · Crystal structure of DpgC with bound substrate analog and Xe on oxygen diffusion pathway · the same entry in another collection · chain G against G, 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 Q8KLK7
Elsewhere: RCSB PDB 4YLH · PDBe 4YLH · UniProt Q8KLK7

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