SMTL ID : 7dka.1

Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, C24S mutant protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

12 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 3 residues within 4Å: Chain A: L.80, R.93, N.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97 Salt bridges: A:R.93 ACT.3: 5 residues within 4Å: Chain A: S.30, P.31, Y.32, T.179 Ligands: ACT.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.179, A:T.179 ACT.5: 3 residues within 4Å: Chain A: L.197, R.199 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.197 Salt bridges: A:R.199 ACT.6: 4 residues within 4Å: Chain A: D.156, A.158, G.159, R.162 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.162 ACT.7: 4 residues within 4Å: Chain A: E.111, K.112, A.115, A.143 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.112 Hydrogen bonds: A:G.144 Water bridges: A:A.115 Salt bridges: A:K.112 ACT.9: 3 residues within 4Å: Chain A: N.61, Y.88 Ligands: ACT.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.88 Hydrogen bonds: A:N.61, A:N.61 ACT.10: 3 residues within 4Å: Chain A: G.87, Y.88, K.90 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.87, A:Y.88 Salt bridges: A:K.90 ACT.11: 2 residues within 4Å: Chain A: D.138, R.142 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.142 Hydrogen bonds: A:D.138 Salt bridges: A:R.142 ACT.12: 6 residues within 4Å: Chain A: L.52, R.53, H.54, H.103, A.106, D.167 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.52 Water bridges: A:H.54, A:S.113, A:S.113, A:S.113 Salt bridges: A:H.54, A:H.103 ACT.15: 4 residues within 4Å: Chain B: H.124, H.125, K.128 Ligands: TRS.14 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:H.124, B:H.125, B:K.128 ACT.16: 5 residues within 4Å: Chain B: Q.20, P.21, D.23, D.183, G.185 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.23 Water bridges: B:D.23, B:G.186, B:G.186 ACT.17: 3 residues within 4Å: Chain B: D.146, S.148, Q.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.149

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

TRS.2: 3 residues within 4Å: Chain A: L.29, Y.91, H.124 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.29, A:Y.88, A:H.124, A:H.124 TRS.14: 6 residues within 4Å: Chain B: L.29, Y.91, H.124, H.125 Ligands: PEG.13, ACT.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.125 Water bridges: B:H.124, B:D.130

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

PEG.4: 8 residues within 4Å: Chain A: L.197, T.198, R.199, D.200, A.203 Chain B: E.218, A.219 Ligands: ACT.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.199, A:D.200, B:E.218 PEG.8: 4 residues within 4Å: Chain A: R.107, G.159, R.162, E.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.107, A:G.159, A:R.162, A:E.163 PEG.13: 5 residues within 4Å: Chain B: L.29, S.30, L.57, N.61 Ligands: TRS.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M.-K. et al., Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein. To Be Published

Release Date

2021-11-24

Peptides

DSBA domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DSBA domain-containing protein