MolNFT v1 · #134129 · protein

Structure of the EXBB/EXBD complex from E. COLI at pH 4.5

5SV1 · Biopolymer transport protein exbb: “Structure of the EXBB/EXBD complex from E. COLI at pH 4.5”. X-ray diffraction, 1 ligand (HG), 20 pockets (best druggability 0.90). MolNFT v1 #134129 on GenesisL1: 3D structure, binding sites and…

PDB: 5SV1
Type: protein
Length: 2,264 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biopolymer transport protein exbb; Biopolymer transport protein exbd
UniProt: P0ABU8, P0ABV4
Ligands: HG
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 11 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Biopolymer transport protein exbb	protein	224	82% helix, 0% strand	P0ABU8
B, G	Biopolymer transport protein exbb	protein	225	82% helix, 0% strand	P0ABU8
C	Biopolymer transport protein exbb	protein	224	84% helix, 0% strand	P0ABU8
D	Biopolymer transport protein exbb	protein	215	83% helix, 0% strand	P0ABU8
E	Biopolymer transport protein exbb	protein	223	83% helix, 0% strand	P0ABU8
F	Biopolymer transport protein exbb	protein	226	82% helix, 0% strand	P0ABU8
H	Biopolymer transport protein exbb	protein	222	85% helix, 0% strand	P0ABU8
I	Biopolymer transport protein exbb	protein	216	82% helix, 0% strand	P0ABU8
J	Biopolymer transport protein exbb	protein	219	82% helix, 0% strand	P0ABU8
Y	Biopolymer transport protein exbd	protein	23	78% helix, 0% strand	P0ABV4
Z	Biopolymer transport protein exbd	protein	22	73% helix, 0% strand	P0ABV4

Ligands and binding sites

HG · Mercury (II) ion · metal · 10 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1020	0.90	0.91	118	empty
2	383	0.84	0.92	59	empty
3	1077	0.83	0.83	122	empty
4	1109	0.73	0.76	96	empty
5	934	0.71	0.76	110	empty

Interfaces

25 interfaces between chains.

F–G · 1638 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1632 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1582 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 1550 Å² buried · 7 hydrogen bonds · protein-protein
H–I · 1527 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (methylation).

Compared structures

5SV1 · Structure of the ExbB/ExbD complex from E. coli at pH 4.5 · the same entry in another collection · chain Z against Z, 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 P0ABU8
Every structure of UniProt P0ABV4
Elsewhere: RCSB PDB 5SV1 · PDBe 5SV1 · UniProt P0ABU8 · UniProt P0ABV4

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