MolNFT v1 · #165628 · protein

Apo form of thermus thermophilus D-alanine-D-alanine ligase

6U1C · D-alanine--D-alanine ligase: “Apo form of thermus thermophilus D-alanine-D-alanine ligase”. X-ray diffraction, 12 pockets (best druggability 0.77). MolNFT v1 #165628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U1C
Type: protein
Length: 1,213 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: D-alanine--D-alanine ligase
EC: 6.3.2.4
UniProt: Q5SHZ3
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-alanine--D-alanine ligase (EC 6.3.2.4)	protein	310	34% helix, 23% strand	Q5SHZ3
B	D-alanine--D-alanine ligase (EC 6.3.2.4)	protein	302	34% helix, 25% strand	Q5SHZ3
C	D-alanine--D-alanine ligase (EC 6.3.2.4)	protein	301	34% helix, 24% strand	Q5SHZ3
D	D-alanine--D-alanine ligase (EC 6.3.2.4)	protein	300	33% helix, 25% strand	Q5SHZ3

Pockets

12 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	810	0.77	0.80	74	empty
2	352	0.73	0.85	42	empty
3	313	0.71	0.84	38	empty
4	387	0.68	0.81	37	empty
5	313	0.58	0.77	39	empty

Interfaces

4 interfaces between chains.

C–D · 1446 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 1446 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 168 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 24 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6U1C · Apo form of Thermus thermophilus D-alanine-D-alanine ligase · the same entry in another collection · chain D against D, TM-score 1.00
Q5SHZ3 · AlphaFold monomer V2.0 prediction for D-alanine--D-alanine ligase (Q5SHZ3) · 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 Q5SHZ3
Elsewhere: RCSB PDB 6U1C · PDBe 6U1C · UniProt Q5SHZ3

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