SMTL ID : 3wgg.1

Crystal structure of RSP in complex with alpha-NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 8NA: alpha-Diphosphopyridine nucleotide(Non-covalent)

8NA.1: 24 residues within 4Å: Chain A: I.90, G.91, G.93, N.94, L.95, F.116, D.117, I.118, N.119, L.122, V.135, C.153, I.154, P.155, N.158, T.162, F.177, P.179 Chain B: A.98, N.101, Y.102, T.103, S.104 Ligands: SO4.3 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.179 Hydrogen bonds: A:N.94, A:L.95, A:I.118, A:N.119, A:I.154, A:K.156, A:N.158, A:T.162, A:T.162, B:N.101, B:S.104, B:S.104 Water bridges: A:G.93, A:N.94, A:G.96, A:N.119, B:Q.97 pi-Stacking: B:Y.102 8NA.5: 21 residues within 4Å: Chain A: A.98, N.101, Y.102, T.103, S.104 Chain B: I.90, G.91, G.93, N.94, L.95, D.117, I.118, N.119, L.122, C.153, I.154, P.155, F.177, L.178, P.179 Ligands: SO4.6 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:Y.102, A:Y.102, B:P.179 Hydrogen bonds: A:N.101, A:S.104, A:S.104, B:N.94, B:N.94, B:L.95, B:I.118, B:N.119, B:I.154, B:K.156 Water bridges: B:G.93, B:G.96, B:N.119, B:N.158, B:N.158, B:T.162

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.17, R.20, Y.21 Chain B: N.192, H.194 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.17, A:R.20, B:H.194 Hydrogen bonds: B:N.192 Water bridges: B:N.192 SO4.3: 7 residues within 4Å: Chain A: P.179, H.194, L.195, S.196 Chain B: Y.102, S.104 Ligands: 8NA.1 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:S.104, A:L.195, A:S.196, A:S.196 Water bridges: A:S.196 Salt bridges: A:H.194 SO4.4: 7 residues within 4Å: Chain A: S.34, S.35, Q.61, Q.62, G.63, Y.64, G.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.34, A:S.35, A:G.63, A:Y.64, A:G.65 SO4.6: 8 residues within 4Å: Chain A: Y.102, S.104 Chain B: P.179, V.193, H.194, L.195, S.196 Ligands: 8NA.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.195, B:S.196, B:S.196, B:S.196, A:S.104 Salt bridges: B:H.194 SO4.7: 5 residues within 4Å: Chain B: S.34, S.35, R.36, R.50, G.65 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.35, B:R.36, B:G.65 Water bridges: B:S.35, B:S.35, B:R.36, B:G.63 Salt bridges: B:R.36, B:R.50 SO4.8: 3 residues within 4Å: Chain A: N.192, H.194 Chain B: R.20 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.192 Salt bridges: A:H.194, B:R.20 Water bridges: B:R.20, B:R.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Y. et al., Binding mode of the oxidized alpha-anomer of NAD(+) to RSP, a Rex-family repressor. Biochem.Biophys.Res.Commun. (2015)

Release Date

2014-08-13

Peptides

Redox-sensing transcriptional repressor rex: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Redox-sensing transcriptional repressor rex

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