MolNFT v1 · #126801 · protein

Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi (crystal form II)

5MDP: “Crystal structure of in vitro folded chitoporin vhchip from vibrio harveyi (crystal form II)”. X-ray diffraction, 14 pockets (best druggability 0.72). MolNFT v1 #126801 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MDP
Type: protein
Length: 1,023 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Chitoporin
UniProt: L0RVU0
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Chitoporin	protein	341	6% helix, 59% strand	L0RVU0

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1055	0.72	0.76	107	empty
2	876	0.70	0.76	93	empty
3	620	0.67	0.77	57	empty
4	196	0.47	0.75	36	empty
5	168	0.44	0.74	24	empty

Interfaces

3 interfaces between chains.

A–B · 1659 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1638 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1636 Å² buried · 21 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 modified (engineered).

Compared structures

5MDP · Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal 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 L0RVU0
Elsewhere: RCSB PDB 5MDP · PDBe 5MDP · UniProt L0RVU0

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