SMTL ID : 4qvb.1

Mycobacterium tuberculosis protein Rv1155 in complex with co-enzyme F420

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: R.108, W.117, R.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108, A:R.121 FMT.2: 3 residues within 4Å: Chain A: D.7, H.138, V.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.7 FMT.3: 5 residues within 4Å: Chain A: K.26, H.27, N.60, R.63 Ligands: F42.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.27, A:R.63, A:R.63 FMT.13: 5 residues within 4Å: Chain B: P.90, P.91, D.97, D.98, T.99 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:P.91, B:A.93, B:D.98, B:T.99, B:T.99 FMT.14: 3 residues within 4Å: Chain B: R.59 Ligands: F42.12, NA.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.59

4 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.4: 4 residues within 4Å: Chain A: D.74, D.75, P.144 Ligands: PGO.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.144 Hydrogen bonds: A:D.74, A:D.75, A:D.75 PDO.5: 2 residues within 4Å: Chain A: D.97, D.98 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.97 Hydrogen bonds: A:D.98, A:D.98 Water bridges: A:D.97 PDO.15: 7 residues within 4Å: Chain A: K.26, D.28, R.30 Chain B: E.83, S.137, H.138 Ligands: EDO.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.26, A:K.26, B:E.83, B:S.137 PDO.16: 4 residues within 4Å: Chain B: S.115, D.116, W.117, D.118 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.117 Hydrogen bonds: B:D.116, B:W.117, B:D.118

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

EDO.6: 2 residues within 4Å: Chain A: W.77 Chain B: I.19 No protein-ligand interaction detected (PLIP) EDO.7: 8 residues within 4Å: Chain A: D.72 Chain B: I.19, G.20, V.21, N.35, L.70, V.71, D.72 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.35, B:L.70, B:D.72, A:D.72 EDO.8: 4 residues within 4Å: Chain A: E.53, R.62, P.91, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.62, A:R.128 EDO.9: 2 residues within 4Å: Chain A: D.28 Ligands: PDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.28 Water bridges: A:D.28, A:D.28

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.10: 4 residues within 4Å: Chain A: A.73, D.74, P.144 Ligands: PDO.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.73, A:D.74 Hydrogen bonds: A:D.74

2 x F42: COENZYME F420(Non-covalent)

F42.11: 20 residues within 4Å: Chain A: K.26, Q.32, S.34, N.35, V.36, Q.37, S.50, I.51, R.55, A.56, K.57, N.60, R.129 Chain B: W.77, S.78, Y.79, H.138, Y.140, L.142 Ligands: FMT.3 24 PLIP interactions: 17 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Q.32, A:N.35, A:A.56, B:W.77, B:L.142 Hydrogen bonds: A:Q.32, A:N.35, A:N.35, A:Q.37, A:S.50, A:R.55, A:A.56, A:K.57, A:K.57, A:N.60, A:R.129, B:W.77, B:Y.79 Water bridges: A:R.129 Salt bridges: A:K.26, A:K.57, B:H.138 pi-Stacking: B:W.77, B:W.77 F42.12: 17 residues within 4Å: Chain A: W.77, Y.79, H.138, Y.140, G.141, L.142 Chain B: K.26, H.27, Q.32, N.35, R.55, A.56, K.57, R.59, N.60 Ligands: FMT.14, NA.17 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.32, B:A.56, A:W.77 Hydrogen bonds: B:H.27, B:Q.32, B:A.56, B:K.57, B:K.57, B:N.60, A:Y.79, A:Y.79 Salt bridges: B:K.26, B:H.27, B:K.57, B:R.59, A:H.138

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

NA.17: 4 residues within 4Å: Chain B: R.55, A.56 Ligands: F42.12, FMT.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.55, B:A.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mashalidis, E.H. et al., Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis. Protein Sci. (2015)

Release Date

2015-02-25

Peptides

Rv1155 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Rv1155 protein