MolNFT v1 · #83952 · protein

Structure of a meso-diaminopimelate dehydrogenase

3WYB · Meso-diaminopimelate D-dehydrogenase: “Structure of a meso-diaminopimelate dehydrogenase”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #83952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3WYB
Type: protein
Length: 654 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Meso-diaminopimelate D-dehydrogenase
EC: 1.4.1.16
UniProt: G1UII1
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Meso-diaminopimelate D-dehydrogenase (EC 1.4.1.16)	protein	327	40% helix, 27% strand	G1UII1

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	711	0.71	0.78	55	empty
2	645	0.70	0.78	53	empty
3	164	0.44	0.74	35	empty
4	82	0.32	0.74	17	empty
5	60	0.30	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 3370 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

3WYB · Structure of a meso-diaminopimelate dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
G1UII1 · AlphaFold monomer V2.0 prediction for meso-diaminopimelate D-dehydrogenase (G1UII1) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 G1UII1
Elsewhere: RCSB PDB 3WYB · PDBe 3WYB · UniProt G1UII1

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