SMTL ID : 6dcf.1

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase and bound to kanglemycin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.45 Å

Oligo State

hetero-1-2-1-1-1-1-mer

Ligands

1 x KNG: Kanglemycin A(Non-covalent)

KNG.1: 15 residues within 4Å: Chain D: R.164, G.423, T.424, S.425, Q.426, S.428, Q.429, F.430, D.432, H.442, R.445, P.480, I.488, R.604, H.671 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Q.426, D:Q.429, D:D.432, D:P.480 Hydrogen bonds: D:R.164, D:Q.429, D:F.430, D:F.430 Salt bridges: D:R.604

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

SO4.2: 3 residues within 4Å: Chain D: H.720, K.888, R.1005 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:H.720, D:K.888, D:R.1005 SO4.3: 2 residues within 4Å: Chain D: R.595, R.916 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.595 SO4.4: 7 residues within 4Å: Chain D: H.832, I.1032, H.1033, A.1034, Q.1053, F.1054, G.1055 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:A.1034, D:F.1054, D:G.1055 Salt bridges: D:H.832, D:H.1033 SO4.8: 2 residues within 4Å: Chain E: H.888, R.1267 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:H.888 Salt bridges: E:R.1267 SO4.9: 2 residues within 4Å: Chain E: R.421, R.427 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.421, E:R.427 SO4.10: 6 residues within 4Å: Chain E: D.882, V.883, T.971, G.972, R.1160, R.1164 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:G.972 Salt bridges: E:R.1160, E:R.1164 SO4.11: 4 residues within 4Å: Chain E: R.894, G.895, K.960, R.1129 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.895, E:G.895 Salt bridges: E:R.894, E:K.960, E:R.1129 SO4.13: 2 residues within 4Å: Chain G: A.254, F.255 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:F.255 SO4.14: 3 residues within 4Å: Chain G: K.210, L.211, V.213 1 PLIP interactions: 1 interactions with chain G Salt bridges: G:K.210

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain E: C.890, R.962, C.967, S.969, C.974, C.977 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.890, E:C.967, E:C.974, E:C.977 ZN.6: 6 residues within 4Å: Chain E: C.60, Y.61, C.62, G.63, C.75, C.78 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.60, E:C.62, E:C.75, E:C.78

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain E: D.535, D.537, D.539 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.535, E:D.535, E:D.537, E:D.539

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.12: 6 residues within 4Å: Chain E: R.886, P.1260, G.1264, I.1265, S.1266, R.1267 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.1265 Hydrogen bonds: E:R.886, E:R.1267 Salt bridges: E:R.886, E:R.1267

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

EDO.15: 7 residues within 4Å: Chain G: L.264, G.265, R.268, W.288, Q.291, A.292 Chain H: G.24 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Hydrogen bonds: G:R.268, G:Q.291, E:R.356 EDO.16: 3 residues within 4Å: Chain G: R.224, D.225, R.228 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.224, G:D.225

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peek, J. et al., Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism. Nat Commun (2018)

Release Date

2018-09-05

Peptides

RNA polymerase-binding protein RbpA: A
DNA-directed RNA polymerase subunit alpha: BC
DNA-directed RNA polymerase subunit beta: D
DNA-directed RNA polymerase subunit beta': E
DNA-directed RNA polymerase subunit omega: F
RNA polymerase sigma factor SigA: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
A

C
B

D
C

E
D

F
E

G
F

RNA polymerase-binding protein RbpA

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma factor SigA

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