MolNFT v1 · #125356 · protein

Structure of caulobacter crescentus VAPBC1 (VAPB1DELTAC:VAPC1 form)

5L6M · Vapb family protein: “Structure of caulobacter crescentus VAPBC1 (VAPB1DELTAC:VAPC1 form)”. X-ray diffraction, 11 pockets (best druggability 0.78). MolNFT v1 #125356 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L6M
Type: protein
Length: 1,173 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vapb family protein; Ribonuclease vapc
EC: 3.1.-.-
UniProt: Q9AC34, Q9AC35
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 27% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vapb family protein	protein	66	15% helix, 39% strand	Q9AC34
B, C, F, G, J, K	Ribonuclease vapc (EC 3.1.-.-)	protein	127	59% helix, 13% strand	Q9AC35
D	Vapb family protein	protein	71	18% helix, 37% strand	Q9AC34
E	Vapb family protein	protein	66	5% helix, 42% strand	Q9AC34
H, L	Vapb family protein	protein	70	19% helix, 40% strand	Q9AC34
I	Vapb family protein	protein	68	19% helix, 43% strand	Q9AC34

Ligands and binding sites

MLI · Malonate ion · additive · 3 copies · chains A, B, D, C, H, G
GOL · Glycerol · additive · 2 copies · chains B, C, D, I, J, K, L

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

Pockets

11 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	792	0.78	0.82	75	empty
2	305	0.69	0.84	41	empty
3	359	0.66	0.80	56	MLI
4	296	0.62	0.80	45	MLI
5	56	0.61	0.91	15	empty

Interfaces

30 interfaces between chains.

E–H · 2081 Å² buried · 46 hydrogen bonds · protein-protein
I–L · 1969 Å² buried · 55 hydrogen bonds · protein-protein
A–D · 1848 Å² buried · 47 hydrogen bonds · protein-protein
I–J · 1405 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1353 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5L6M · Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form) · the same entry in another collection · chain A against A, 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 Q9AC34
Every structure of UniProt Q9AC35
Elsewhere: RCSB PDB 5L6M · PDBe 5L6M · UniProt Q9AC34 · UniProt Q9AC35

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