SMTL ID : 7yz9.1

Structure of catalytic domain of Rv1625c bound to nanobody NB4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.81, I.82, D.125 Ligands: MN.3, ONM.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.81, A:I.82 MN.2: 1 residues within 4Å: Chain A: D.102 No protein-ligand interaction detected (PLIP) MN.3: 4 residues within 4Å: Chain A: D.81, D.125 Ligands: MN.1, ONM.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.81, A:D.125

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: R.103, S.106, A.107 Chain B: R.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.103, B:R.103 GOL.5: 4 residues within 4Å: Chain A: K.119, R.186, F.187, F.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.119, A:R.186, A:R.186, A:R.186

1 x ONM: 3'-O-(N-METHYLANTHRANILOYL)-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

ONM.6: 12 residues within 4Å: Chain A: D.81, I.82, V.83, G.84, F.85, T.86, A.89, S.90, D.125, R.169 Ligands: MN.1, MN.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.81, A:G.84, A:F.85, A:T.86 Water bridges: A:E.87, A:R.169, A:R.169 Salt bridges: A:R.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mehta, V. et al., Structure of Mycobacterium tuberculosis Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases. Elife (2022)

Release Date

2022-08-31

Peptides

Adenylate cyclase: A
nanobody NB4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenylate cyclase

nanobody NB4

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