SMTL ID : 7r4w.1

Single stranded DNA binding protein SSB M5 from Fervidobacterium gondwanense

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 3 residues within 4Å: Chain A: F.51, R.52, W.93 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.93 Salt bridges: A:R.52 ACY.2: 3 residues within 4Å: Chain A: R.19, T.21, L.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.22 Hydrogen bonds: A:L.22 Salt bridges: A:R.19 ACY.4: 3 residues within 4Å: Chain B: F.51, R.52, W.93 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.93 Salt bridges: B:R.52 ACY.5: 3 residues within 4Å: Chain B: R.19, T.21, L.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.22 Hydrogen bonds: B:L.22 Salt bridges: B:R.19 ACY.7: 3 residues within 4Å: Chain C: F.51, R.52, W.93 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.93 Salt bridges: C:R.52 ACY.8: 3 residues within 4Å: Chain C: R.19, T.21, L.22 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.22 Hydrogen bonds: C:L.22 Salt bridges: C:R.19 ACY.10: 3 residues within 4Å: Chain D: F.51, R.52, W.93 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:W.93 Salt bridges: D:R.52 ACY.11: 3 residues within 4Å: Chain D: R.19, T.21, L.22 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.22 Hydrogen bonds: D:L.22 Salt bridges: D:R.19

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: K.5, K.73, D.95 Chain D: D.71, D.95, N.96 Ligands: PO4.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Water bridges: A:K.73, D:N.96 Salt bridges: A:K.5, A:K.73 Hydrogen bonds: D:D.71, D:N.96 PO4.6: 7 residues within 4Å: Chain B: K.5, K.73, D.95 Chain C: D.71, D.95, N.96 Ligands: PO4.9 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.71, C:N.96 Water bridges: C:N.96, B:K.73 Salt bridges: B:K.5, B:K.73 PO4.9: 7 residues within 4Å: Chain B: D.71, D.95, N.96 Chain C: K.5, K.73, D.95 Ligands: PO4.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:D.71, B:N.96 Water bridges: B:N.96, C:K.73 Salt bridges: C:K.5, C:K.73 PO4.12: 7 residues within 4Å: Chain A: D.71, D.95, N.96 Chain D: K.5, K.73, D.95 Ligands: PO4.3 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:D.71, A:N.96 Water bridges: A:N.96, D:K.73 Salt bridges: D:K.5, D:K.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werbowy, O. et al., Molecular characterization of a single stranded DNA binding protein from Fervidobacterium gondwanense. To Be Published

Release Date

2023-08-23

Peptides

Single-stranded DNA-binding protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Single-stranded DNA-binding protein