SMTL ID : 6zt3.1

N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed with ADPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 26 residues within 4Å: Chain A: E.49, N.53, E.57, D.80, G.84, I.85, V.100, A.106, G.107, G.108, K.109, Y.115, G.120, L.121, H.122, G.123, V.124, G.125, V.126, T.170, Q.371, K.373 Chain B: Y.13, I.18 Ligands: MG.2, K.11 25 PLIP interactions: 1 interactions with chain B, 24 interactions with chain A Hydrogen bonds: B:Y.13, A:E.49, A:N.53, A:D.80, A:G.108, A:K.109, A:K.109, A:Y.115, A:L.121, A:H.122, A:G.123, A:V.124, A:G.125, A:V.126, A:T.170, A:Q.371, A:K.373, A:K.373 Water bridges: A:E.49, A:E.49, A:A.54, A:G.107, A:G.107, A:K.109 pi-Cation interactions: A:K.109 ANP.12: 26 residues within 4Å: Chain A: Y.13, I.18 Chain B: E.49, N.53, E.57, D.80, G.84, I.85, V.100, A.106, G.107, G.108, K.109, Y.115, G.120, L.121, H.122, G.123, V.124, G.125, V.126, T.170, Q.371, K.373 Ligands: MG.13, K.22 26 PLIP interactions: 25 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.49, B:N.53, B:E.57, B:D.80, B:G.108, B:K.109, B:K.109, B:L.121, B:H.122, B:G.123, B:V.124, B:G.125, B:V.126, B:Q.371, B:K.373, B:K.373, A:Y.13 Water bridges: B:E.49, B:N.53, B:A.54, B:D.80, B:G.107, B:K.109, B:T.170, B:T.170 pi-Cation interactions: B:K.109

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: N.53, K.109 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain B: N.53, K.109 Ligands: ANP.12 No protein-ligand interaction detected (PLIP)

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

EDO.3: 5 residues within 4Å: Chain A: E.137, A.138, T.139, T.171, R.173 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.138, A:T.139 Water bridges: A:E.77 EDO.4: 4 residues within 4Å: Chain A: D.67, K.69, E.77, R.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.69, A:K.69 Water bridges: A:R.79, A:R.79 EDO.5: 6 residues within 4Å: Chain A: V.117, G.285, H.286, E.287, K.362, A.364 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.287 Water bridges: A:G.285, A:H.286 EDO.6: 3 residues within 4Å: Chain A: W.48, R.194, H.312 4 PLIP interactions: 4 interactions with chain A Water bridges: A:W.48, A:E.197, A:N.310, A:T.372 EDO.7: 7 residues within 4Å: Chain A: H.45, W.48, E.49, D.52, I.309, Q.371, K.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.49 Water bridges: A:R.194, A:R.194 EDO.14: 5 residues within 4Å: Chain B: E.137, A.138, T.139, T.171, R.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.138, B:T.139 Water bridges: B:E.77 EDO.15: 4 residues within 4Å: Chain B: D.67, K.69, E.77, R.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.69, B:K.69, B:E.77 Water bridges: B:R.79, B:R.79 EDO.16: 6 residues within 4Å: Chain B: V.117, G.285, H.286, E.287, K.362, A.364 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.287, B:E.287 Water bridges: B:G.285, B:H.286 EDO.17: 3 residues within 4Å: Chain B: W.48, R.194, H.312 4 PLIP interactions: 4 interactions with chain B Water bridges: B:W.48, B:E.197, B:N.310, B:T.372 EDO.18: 7 residues within 4Å: Chain B: H.45, W.48, E.49, D.52, I.309, Q.371, K.373 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.49, B:D.52 Water bridges: B:R.194, B:R.194

6 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: K.109, D.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.109 NA.9: 3 residues within 4Å: Chain A: D.81, G.82, T.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.81, A:T.168 NA.10: 2 residues within 4Å: Chain A: K.6, N.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.6, A:K.6 NA.19: 2 residues within 4Å: Chain B: K.109, D.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.109 NA.20: 3 residues within 4Å: Chain B: D.81, G.82, T.168 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.82, B:T.168, B:T.168 NA.21: 2 residues within 4Å: Chain B: K.6, N.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.6, B:K.6

2 x K: POTASSIUM ION(Non-covalent)

K.11: 7 residues within 4Å: Chain A: V.100, Q.103, A.106, G.123, V.124, S.127 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.100, A:A.106, A:G.123 K.22: 7 residues within 4Å: Chain B: V.100, Q.103, A.106, G.123, V.124, S.127 Ligands: ANP.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.100, B:A.106, B:G.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, L. et al., The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-03-03

Peptides

DNA gyrase subunit B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA gyrase subunit B

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