SMTL ID : 3ib8.1

Crystal structure of full length Rv0805 in complex with 5'-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: D.33, H.35, D.75, H.221 Ligands: MN.2, AMP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.33, A:H.35, A:D.75, A:H.221, H2O.10 FE.9: 6 residues within 4Å: Chain B: D.33, H.35, D.75, H.221 Ligands: MN.10, AMP.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.33, B:H.35, B:D.75, B:H.221, H2O.19

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: D.75, N.109, H.181, H.219 Ligands: FE.1, AMP.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.75, A:H.181, A:H.219, AMP.3, H2O.10 MN.10: 6 residues within 4Å: Chain B: D.75, N.109, H.181, H.219 Ligands: FE.9, AMP.11 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.75, B:H.181, B:H.219, AMP.11, H2O.19

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 15 residues within 4Å: Chain A: H.35, D.75, N.109, H.110, M.191, A.192, T.194, V.195, H.219, L.220, H.221, Q.243, T.252 Ligands: FE.1, MN.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.109, A:N.109, A:H.219, A:Q.243 Water bridges: A:Y.241, A:Y.241, A:Y.241 Salt bridges: A:H.35, A:H.110, A:H.219, A:H.221 AMP.11: 15 residues within 4Å: Chain B: H.35, D.75, N.109, H.110, M.191, A.192, T.194, V.195, H.219, L.220, H.221, Q.243, T.252 Ligands: FE.9, MN.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.109, B:N.109, B:T.194, B:H.219, B:Q.243 Water bridges: B:Y.44, B:Y.241, B:Y.241, B:Y.241 Salt bridges: B:H.35, B:H.110, B:H.219, B:H.221

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.4: 9 residues within 4Å: Chain A: D.78, K.79, N.109, H.110, D.111, P.149, G.150, H.151, H.152 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.78, A:G.150, A:G.150 Water bridges: A:N.109, A:D.111, A:D.112, A:V.148 BTB.12: 9 residues within 4Å: Chain B: D.78, K.79, N.109, H.110, D.111, P.149, G.150, H.151, H.152 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.78, B:G.150, B:G.150 Water bridges: B:N.109, B:D.111, B:V.148

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 6 residues within 4Å: Chain A: V.104, W.105, L.121, R.132, C.134, V.143 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.121, A:R.132, A:V.143 Hydrogen bonds: A:W.105 Water bridges: A:R.132, A:R.132 MPD.6: 5 residues within 4Å: Chain A: P.129, D.131, S.159, Q.160, W.163 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.131, A:W.163 Hydrogen bonds: A:D.131, A:D.131, A:R.157 MPD.7: 5 residues within 4Å: Chain A: R.89, E.93, L.103, W.105, L.121 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.103 Hydrogen bonds: A:E.93, A:W.105 Water bridges: A:E.93 MPD.13: 6 residues within 4Å: Chain B: V.104, W.105, L.121, R.132, C.134, V.143 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.121, B:R.132, B:V.143 Hydrogen bonds: B:W.105 Water bridges: B:R.132, B:R.132 MPD.14: 5 residues within 4Å: Chain B: P.129, D.131, S.159, Q.160, W.163 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.131, B:W.163 Hydrogen bonds: B:D.131, B:R.157 MPD.15: 5 residues within 4Å: Chain B: R.89, E.93, L.103, W.105, L.121 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.103 Hydrogen bonds: B:E.93, B:W.105

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

ACT.8: 3 residues within 4Å: Chain A: A.172, G.175, R.213 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.213 Hydrogen bonds: A:A.172, A:G.175 ACT.16: 3 residues within 4Å: Chain B: A.172, G.175, R.213 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.213 Hydrogen bonds: B:A.172, B:G.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Podobnik, M. et al., A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability. J.Biol.Chem. (2009)

Release Date

2009-09-29

Peptides

Icc protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Icc protein

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