SMTL ID : 7wup.1

The crystal structure of ApiI

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: I.98, K.99, K.101, I.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.98, A:K.101 EDO.7: 5 residues within 4Å: Chain B: G.266, A.268, D.292, F.318, C.335 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.292, B:L.293

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: V.367, I.393, V.410 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.368 GOL.4: 5 residues within 4Å: Chain A: K.389 Chain B: N.126, T.129, R.130, W.133 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:N.126, B:T.129, A:K.389, A:E.390 Hydrogen bonds: A:K.389, A:K.389

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: G.266, D.292, L.293, V.296, F.318, C.335, Y.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.293, A:Y.339, A:Y.339

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: N.126, R.130 Chain B: K.389 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain A: M.167, I.170, G.171, M.378, L.382 Chain B: R.78, L.81, G.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, J. et al., The crystal structure of ApiI. To Be Published

Release Date

2023-02-15

Peptides

ApiI: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ApiI