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Crystal structure of the alcanivorax borkumensis ydah transporter reveals an unusual topology

Analyse Crystal structure of the alcanivorax borkumensis ydah transporter reveals an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R0C
Type: protein
Length: 1,901 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Abgt putative transporter family
UniProt: Q0VR69
Ligands: NA
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Abgt putative transporter family	protein	476	70% helix, 0% strand	Q0VR69
B	Abgt putative transporter family	protein	468	71% helix, 1% strand	Q0VR69
C	Abgt putative transporter family	protein	474	72% helix, 1% strand	Q0VR69
D	Abgt putative transporter family	protein	483	70% helix, 1% strand	Q0VR69

Ligands and binding sites

NA · Sodium ion · metal · 4 copies · chains A, B, C, D
LMT · Dodecyl-beta-D-maltoside · additive · 6 copies · chains A, B, C, D
BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, C, D

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	868	0.76	0.79	71	empty
2	823	0.76	0.79	68	LMT
3	770	0.76	0.80	67	empty
4	806	0.75	0.79	67	LMT, BOG
5	647	0.74	0.80	54	empty

Interfaces

3 interfaces between chains.

C–D · 1770 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 1770 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 1117 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4R0C · Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual… · the same entry in another collection · chain D against D, 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 Q0VR69
Elsewhere: RCSB PDB 4R0C · PDBe 4R0C · UniProt Q0VR69

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