SMTL ID : 3hss.1

A higher resolution structure of Rv0554 from Mycobacterium tuberculosis complexed with malonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 9 residues within 4Å: Chain A: G.51, R.52, S.118, M.119, R.144, Q.214, L.215, C.217 Ligands: ACT.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.52, A:M.119, A:Q.214 Water bridges: A:R.52, A:S.118, A:R.144, A:R.144

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

EDO.2: 5 residues within 4Å: Chain A: L.178, L.187, V.193 Chain B: R.149, A.150 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.175, A:L.187 EDO.4: 7 residues within 4Å: Chain A: R.52, G.53, G.54, T.58, L.271 Ligands: MLA.3, EDO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.51 EDO.5: 3 residues within 4Å: Chain A: R.52, I.205 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.52 EDO.6: 3 residues within 4Å: Chain A: A.192, D.195, W.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195 EDO.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: G.43, D.44, G.71, Y.72 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.44, B:D.44 Water bridges: B:T.42, B:G.71, B:Y.72, B:Y.72, B:R.113

3 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 6 residues within 4Å: Chain A: T.58, R.177, W.203, L.271, F.274 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.203 Water bridges: A:R.177 Salt bridges: A:R.177 MLA.10: 7 residues within 4Å: Chain B: G.51, R.52, S.118, M.119, R.151, F.154, H.270 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.52 Hydrogen bonds: B:R.52, B:S.118, B:S.118, B:M.119 Water bridges: B:R.151, B:R.151, B:C.217 Salt bridges: B:R.151, B:H.270 MLA.13: 6 residues within 4Å: Chain B: T.58, R.177, M.199, W.203, L.271, F.274 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.203 Salt bridges: B:R.177

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

NA.7: 4 residues within 4Å: Chain A: A.254, D.255, L.257, G.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.255, A:G.260 NA.12: 4 residues within 4Å: Chain B: A.254, D.255, L.257, G.260 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.260, B:G.260 Water bridges: B:D.255

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

ACT.8: 6 residues within 4Å: Chain A: R.144, L.147, N.155, L.215, A.218 Ligands: TRS.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.147, A:N.155 Hydrogen bonds: A:L.215 Water bridges: A:R.144 Salt bridges: A:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnston, J.M. et al., Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-05-26

Peptides

putative Bromoperoxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

putative Bromoperoxidase

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