SMTL ID : 5c8a.1

Crystal structure of a truncated form of Thermus thermophilus CarH bound to adenosylcobalamin (dark state)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 31 residues within 4Å: Chain A: L.42, L.45, R.46, G.49, E.50, W.52, H.53, E.62, H.63, S.66, R.70, G.95, E.96, R.97, H.98, E.99, I.100, G.101, V.141, L.142, S.143, V.145, L.146, E.148, G.168, G.169, Q.170, M.185, D.187, L.188 Ligands: 5AD.2 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.141, A:V.145, A:L.146, A:L.146, A:M.185, A:L.188 Hydrogen bonds: A:R.46, A:R.70, A:G.95, A:R.97, A:H.98, A:E.99, A:E.99, A:I.100, A:Q.170 Water bridges: A:R.46, A:R.46, A:E.50, A:E.50, A:R.97, B:R.70 Salt bridges: A:R.46 Metal complexes: A:H.98 B12.3: 31 residues within 4Å: Chain B: L.42, L.45, R.46, G.49, E.50, W.52, H.53, E.62, H.63, S.66, R.70, G.95, E.96, R.97, H.98, E.99, I.100, G.101, L.104, V.141, L.142, S.143, V.145, L.146, G.168, G.169, Q.170, M.185, D.187, L.188 Ligands: 5AD.4 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.42, B:L.104, B:V.141, B:V.145, B:L.146, B:L.146, B:M.185, B:L.188 Hydrogen bonds: B:R.46, B:E.50, B:R.70, B:G.95, B:R.97, B:H.98, B:E.99, B:E.99, B:I.100, B:Q.170 Water bridges: B:Q.170 Salt bridges: B:R.46 Metal complexes: B:H.98 B12.6: 30 residues within 4Å: Chain C: L.42, L.45, R.46, G.49, E.50, W.52, H.53, E.62, H.63, S.66, R.70, G.95, E.96, R.97, H.98, E.99, I.100, G.101, V.141, L.142, S.143, V.145, L.146, G.168, G.169, Q.170, M.185, D.187, L.188 Ligands: 5AD.7 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:V.141, C:V.145, C:L.146, C:L.146, C:M.185, C:L.188 Hydrogen bonds: C:R.46, C:H.53, C:R.70, C:G.95, C:R.97, C:H.98, C:E.99, C:E.99, C:E.99, C:I.100, C:Q.170 Water bridges: C:R.46, C:R.97, D:R.70 Metal complexes: C:H.98 B12.8: 30 residues within 4Å: Chain D: L.42, L.45, R.46, G.49, W.52, H.53, E.62, H.63, S.66, R.70, G.95, E.96, R.97, H.98, E.99, I.100, G.101, L.104, V.141, L.142, S.143, V.145, L.146, G.168, G.169, Q.170, M.185, D.187, L.188 Ligands: 5AD.9 23 PLIP interactions: 22 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:L.104, D:V.141, D:V.145, D:L.146, D:L.146, D:M.185, D:L.188 Hydrogen bonds: D:R.46, D:E.50, D:H.53, D:R.70, D:G.95, D:R.97, D:H.98, D:E.99, D:E.99, D:E.99, D:I.100, D:Q.170 Water bridges: D:Q.170, C:R.70 Salt bridges: D:R.46 Metal complexes: D:H.98

4 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 7 residues within 4Å: Chain A: W.52, V.59, E.62, H.63 Chain B: D.122, P.124 Ligands: B12.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.59 Water bridges: A:R.97, B:D.122 5AD.4: 7 residues within 4Å: Chain A: D.122, P.124 Chain B: W.52, V.59, E.62, H.63 Ligands: B12.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.59 5AD.7: 7 residues within 4Å: Chain C: W.52, V.59, E.62, H.63 Chain D: D.122, P.124 Ligands: B12.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.59, C:E.62 5AD.9: 7 residues within 4Å: Chain C: D.122, P.124 Chain D: W.52, V.59, E.62, H.63 Ligands: B12.8 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.59, D:E.62 Water bridges: D:R.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: K.159, A.162, P.163, R.164, V.165, G.181, E.183 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.159, B:A.162, B:V.165, B:V.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jost, M. et al., Structural basis for gene regulation by a B12-dependent photoreceptor. Nature (2015)

Release Date

2015-09-30

Peptides

Light-dependent transcriptional regulator CarH: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Light-dependent transcriptional regulator CarH