SMTL ID : 5c8d.1 (1 other biounit)

Crystal structure of full-length Thermus thermophilus CarH bound to adenosylcobalamin (dark state)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 28 residues within 4Å: Chain A: E.137, L.141, L.144, G.148, W.151, E.161, H.162, S.165, G.194, E.195, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, G.267, G.268, Q.269, M.284, D.286, L.287 Ligands: 5AD.2 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.141, A:V.240, A:V.244, A:L.245, A:L.245, A:M.284, A:L.287 Hydrogen bonds: A:E.137, A:G.194, A:R.196, A:E.198, A:E.198, A:I.199, A:Q.269, A:Q.269 Metal complexes: A:H.197 B12.3: 32 residues within 4Å: Chain B: L.141, L.144, R.145, G.148, E.149, W.151, H.152, E.161, H.162, S.165, R.169, G.194, E.195, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, G.267, G.268, Q.269, M.284, D.286, L.287, L.290 Ligands: 5AD.4 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:L.141, B:L.203, B:V.240, B:V.244, B:L.245, B:L.245, B:M.284, B:L.287, B:L.290 Hydrogen bonds: B:R.145, B:E.149, B:R.169, B:G.194, B:R.196, B:H.197, B:E.198, B:E.198, B:I.199, B:Q.269 Salt bridges: B:R.145 Metal complexes: B:H.197 B12.5: 30 residues within 4Å: Chain C: E.137, L.141, L.144, R.145, G.148, E.149, W.151, H.152, E.161, H.162, S.165, G.194, E.195, R.196, H.197, E.198, I.199, G.200, L.203, V.240, S.242, V.244, L.245, G.267, G.268, Q.269, M.284, D.286, L.287 Ligands: 5AD.6 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:W.151, C:W.151, C:V.240, C:V.244, C:V.244, C:L.245, C:L.245, C:M.284, C:L.287 Hydrogen bonds: C:E.137, C:R.145, C:E.149, C:G.194, C:R.196, C:H.197, C:E.198, C:E.198, C:E.198, C:I.199, C:Q.269 Salt bridges: C:R.145 Metal complexes: C:H.197 B12.7: 32 residues within 4Å: Chain D: E.137, L.141, L.144, R.145, G.148, E.149, W.151, H.152, E.161, H.162, S.165, R.169, G.194, E.195, R.196, H.197, E.198, I.199, G.200, V.240, L.241, S.242, V.244, L.245, G.267, G.268, Q.269, M.284, D.286, L.287, L.290 Ligands: 5AD.8 23 PLIP interactions: 23 interactions with chain D, Hydrophobic interactions: D:R.196, D:V.240, D:V.244, D:L.245, D:L.245, D:M.284, D:L.287, D:L.290 Hydrogen bonds: D:E.137, D:R.145, D:E.149, D:H.152, D:R.169, D:G.194, D:R.196, D:H.197, D:E.198, D:E.198, D:I.199, D:G.200, D:Q.269 Salt bridges: D:R.145 Metal complexes: D:H.197

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

5AD.2: 7 residues within 4Å: Chain A: W.151, V.158, E.161, H.162 Chain B: D.221, P.223 Ligands: B12.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.158 5AD.4: 7 residues within 4Å: Chain A: D.221, P.223 Chain B: W.151, V.158, E.161, H.162 Ligands: B12.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.158 5AD.6: 7 residues within 4Å: Chain C: W.151, V.158, E.161, H.162 Chain D: D.221, P.223 Ligands: B12.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.158, C:E.161 5AD.8: 7 residues within 4Å: Chain C: D.221, P.223 Chain D: W.151, V.158, E.161, H.162 Ligands: B12.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.158, D:E.161

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

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