SMTL ID : 7f6u.1

Crystal structure of metal-citrate-binding mutant (Y221A) protein (MctA) of ABC transporter in apo state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: A.108, R.111, G.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.108, A:G.113 NA.2: 4 residues within 4Å: Chain A: S.200, T.201, G.202 Ligands: CAC.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.200, A:G.202 Water bridges: A:S.200

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

SO4.3: 4 residues within 4Å: Chain A: P.139, T.140, T.141, G.144 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.140, A:T.141, A:T.141, A:G.144 Water bridges: A:T.140, A:T.140

1 x CO2: CARBON DIOXIDE(Non-covalent)

CO2.4: 2 residues within 4Å: Chain A: P.107, A.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.108 Water bridges: A:N.109

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

EDO.5: 5 residues within 4Å: Chain A: F.180, D.241, D.308, K.309, Y.311 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: Y.177, D.178, P.181, Q.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.184 EDO.7: 3 residues within 4Å: Chain A: G.93, Y.94, R.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.93, A:R.255, A:R.255 EDO.8: 6 residues within 4Å: Chain A: P.163, E.164, S.166, A.167, F.170, R.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.163, A:R.328, A:R.328 Water bridges: A:E.84

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 6 residues within 4Å: Chain A: E.122, F.220, A.223, I.246, R.248 Ligands: CAC.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.223, A:R.248 Water bridges: A:F.220

1 x BGQ: 2-HYDROXY BUTANE-1,4-DIOL(Non-covalent)

BGQ.10: 4 residues within 4Å: Chain A: N.105, L.272, R.288, T.290 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.290 Hydrogen bonds: A:N.105, A:R.288, A:R.288 Water bridges: A:N.105, A:N.105

1 x 1MI: 2-(hydroxymethyl)butane-1,4-diol(Non-covalent)

1MI.11: 5 residues within 4Å: Chain A: L.272, N.276, T.290, V.291, V.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.292 Water bridges: A:N.276, A:N.276

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.12: 5 residues within 4Å: Chain A: W.161, S.200, T.201 Ligands: NA.2, PEG.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.201 Water bridges: A:S.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mandal, S.K. et al., Structural and thermodynamic insights into a novel Mg 2+ -citrate-binding protein from the ABC transporter superfamily. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-12-01

Peptides

Iron ABC transporter, periplasmic iron-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Iron ABC transporter, periplasmic iron-binding protein