SMTL ID : 9g2a.1

Staphylococcus aureus MazF in complex with nanobody 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 9 residues within 4Å: Chain A: S.31, E.32, Q.33 Chain B: P.52 Chain C: W.102, G.103, C.104, I.105 Ligands: MPO.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:I.105, A:E.32 Water bridges: A:G.34 EPE.3: 11 residues within 4Å: Chain A: P.52 Chain B: S.31, E.32, Q.33, G.34, Q.91 Chain D: W.102, G.103, C.104, I.105 Ligands: MPO.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:G.34, D:C.104, D:I.105 Water bridges: B:E.32 pi-Cation interactions: D:W.102, D:W.102

2 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.2: 10 residues within 4Å: Chain A: S.31, Q.33 Chain B: Y.50, S.51, P.52 Chain C: W.102, G.103, C.104, I.105 Ligands: EPE.1 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.105 pi-Cation interactions: C:W.102 MPO.4: 9 residues within 4Å: Chain A: P.52 Chain B: S.31, Q.33, Q.91 Chain D: W.102, G.103, C.104, I.105 Ligands: EPE.3 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain D Water bridges: B:Q.33, D:C.104, D:C.104 Hydrogen bonds: D:I.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prolic-Kalinsek, M. et al., Staphylococcus aureus MazF in complex with nanobody 4. To Be Published

Release Date

2024-07-17

Peptides

Endoribonuclease MazF: AB
Nanobody 4: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Endoribonuclease MazF

Nanobody 4

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