SMTL ID : 8c5p.1

E. coli NfsB mutant N71S T41L with acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 23 residues within 4Å: Chain A: R.10, H.11, S.12, K.14, K.74, Y.144, V.162, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Chain B: P.38, S.39, S.40, L.41, N.42, Q.142, L.145 Ligands: EDO.9, ACT.12 24 PLIP interactions: 18 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.144, A:P.163, A:E.165, B:L.145 Hydrogen bonds: A:S.12, A:S.12, A:S.12, A:S.12, A:K.14, A:K.14, A:K.74, A:K.74, A:E.165, A:G.166, A:N.200, B:S.39, B:L.41, B:N.42 Water bridges: A:R.207, B:E.102, B:R.107 Salt bridges: A:R.10, A:K.205, A:R.207 FMN.8: 22 residues within 4Å: Chain A: P.38, S.39, S.40, L.41, N.42, Q.142, L.145 Chain B: R.10, H.11, S.12, K.14, K.74, Y.144, V.162, P.163, I.164, E.165, G.166, N.200, K.205, R.207 Ligands: ACT.7 24 PLIP interactions: 17 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.144, B:P.163, B:E.165, A:L.145 Hydrogen bonds: B:S.12, B:S.12, B:S.12, B:S.12, B:K.14, B:K.74, B:E.165, B:G.166, B:N.200, A:S.39, A:L.41, A:N.42 Water bridges: B:K.74, B:R.207, A:L.41, A:E.102, A:E.102 Salt bridges: B:R.10, B:K.205, B:R.207

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

EDO.2: 4 residues within 4Å: Chain A: Y.68, F.167, A.169 Ligands: DMS.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.68, A:Y.68, A:A.169 Water bridges: A:A.170 EDO.4: 5 residues within 4Å: Chain A: D.92, L.95, K.96, D.118, K.122 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: R.10, A.155, G.158, L.159, D.160 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.9, A:G.158 Water bridges: A:H.11, A:H.11, A:G.158 EDO.9: 6 residues within 4Å: Chain B: L.41, N.42, E.102, N.117, R.121 Ligands: FMN.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.102, B:N.117, B:R.121 Water bridges: B:L.41, B:E.102, B:R.107 EDO.11: 5 residues within 4Å: Chain B: K.9, H.11, A.201, L.203, K.205 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.11

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: K.179, G.182 No protein-ligand interaction detected (PLIP) DMS.5: 5 residues within 4Å: Chain A: E.165, F.167, A.169, L.186 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.144

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

ACT.7: 4 residues within 4Å: Chain A: S.40, L.41, F.124 Ligands: FMN.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.124 Hydrogen bonds: A:S.40 Water bridges: A:L.41 ACT.10: 5 residues within 4Å: Chain B: K.9, R.10, H.11, L.159, D.160 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.11 Water bridges: B:A.161 Salt bridges: B:H.11 ACT.12: 5 residues within 4Å: Chain A: G.166 Chain B: S.40, L.41, F.124 Ligands: FMN.1 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.124 Hydrogen bonds: B:S.40 Water bridges: B:L.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Day, M.A. et al., Structure and Dynamics of Three Escherichia coli NfsB Nitro-Reductase Mutants Selected for Enhanced Activity with the Cancer Prodrug CB1954. Int J Mol Sci (2023)

Release Date

2023-04-19

Peptides

Oxygen-insensitive NAD(P)H nitroreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Oxygen-insensitive NAD(P)H nitroreductase

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