SMTL ID : 5yk0.2 (1 other biounit)

The complex structure of Rv3197-ADP from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 14 residues within 4Å: Chain A: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.144, A:S.144, A:Q.247, A:I.250, A:D.309 Water bridges: A:I.145, A:K.162, A:K.162, A:E.215, A:G.295, A:D.309 Salt bridges: A:K.162, A:K.162 ADP.11: 14 residues within 4Å: Chain B: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.144, B:S.144, B:Q.247, B:I.250, B:D.309 Water bridges: B:I.145, B:K.162, B:K.162, B:E.215, B:G.295, B:D.309 Salt bridges: B:K.162, B:K.162 ADP.21: 14 residues within 4Å: Chain C: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:S.144, C:S.144, C:Q.247, C:I.250, C:D.309 Water bridges: C:I.145, C:K.162, C:K.162, C:E.215, C:G.295, C:D.309 Salt bridges: C:K.162, C:K.162 ADP.31: 14 residues within 4Å: Chain D: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:S.144, D:S.144, D:Q.247, D:I.250, D:D.309, D:D.309 Water bridges: D:I.145, D:K.162, D:K.162, D:E.215, D:G.295, D:D.309 Salt bridges: D:K.162, D:K.162 ADP.41: 14 residues within 4Å: Chain E: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.144, E:S.144, E:Q.247, E:I.250, E:D.309, E:D.309 Water bridges: E:I.145, E:K.162, E:K.162, E:E.215, E:G.295, E:D.309 Salt bridges: E:K.162, E:K.162 ADP.51: 14 residues within 4Å: Chain F: A.141, S.142, A.143, S.144, V.148, A.160, K.162, P.235, Q.247, E.248, W.249, I.250, I.308, D.309 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.144, F:S.144, F:Q.247, F:I.250, F:D.309, F:D.309 Water bridges: F:I.145, F:K.162, F:K.162, F:E.215, F:G.295, F:D.309 Salt bridges: F:K.162, F:K.162

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

SO4.2: 3 residues within 4Å: Chain A: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: R.131, W.153 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain A: H.229, R.284 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: V.195, Q.196, G.197, D.200 Chain D: R.393 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: K.103, R.118 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain A: R.213 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain B: R.131, W.153 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: H.229, R.284 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: V.195, Q.196, G.197, D.200 Chain F: R.393 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: K.103, R.118 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain B: R.213 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain C: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain C: R.131, W.153 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: H.229, R.284 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain C: V.195, Q.196, G.197, D.200 Chain E: R.393 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain C: K.103, R.118 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain C: R.213 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain D: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain D: R.131, W.153 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain D: H.229, R.284 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain A: R.393 Chain D: V.195, Q.196, G.197, D.200 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain D: K.103, R.118 Ligand excluded by PLIP SO4.37: 1 residues within 4Å: Chain D: R.213 Ligand excluded by PLIP SO4.42: 3 residues within 4Å: Chain E: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.43: 2 residues within 4Å: Chain E: R.131, W.153 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain E: H.229, R.284 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain C: R.393 Chain E: V.195, Q.196, G.197, D.200 Ligand excluded by PLIP SO4.46: 2 residues within 4Å: Chain E: K.103, R.118 Ligand excluded by PLIP SO4.47: 1 residues within 4Å: Chain E: R.213 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain F: Q.350, R.351, Q.403 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain F: R.131, W.153 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain F: H.229, R.284 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain B: R.393 Chain F: V.195, Q.196, G.197, D.200 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain F: K.103, R.118 Ligand excluded by PLIP SO4.57: 1 residues within 4Å: Chain F: R.213 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain A: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain B: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain C: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain C: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain D: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.39: 7 residues within 4Å: Chain D: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain D: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain E: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.49: 7 residues within 4Å: Chain E: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.50: 5 residues within 4Å: Chain E: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP GOL.58: 4 residues within 4Å: Chain F: R.131, R.220, A.239, S.240 Ligand excluded by PLIP GOL.59: 7 residues within 4Å: Chain F: P.282, R.283, L.285, G.286, P.317, G.318, G.319 Ligand excluded by PLIP GOL.60: 5 residues within 4Å: Chain F: D.268, L.269, T.272, H.430, P.432 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Q. et al., Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target. Protein Cell (2018)

Release Date

2018-02-07

Peptides

Probable conserved ATP-binding protein ABC transporter: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Probable conserved ATP-binding protein ABC transporter

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