SMTL ID : 5c8f.2 (1 other biounit)

Crystal structure of light-exposed full-length Thermus thermophilus CarH bound to cobalamin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 28 residues within 4Å: Chain A: L.144, R.145, G.148, E.149, W.151, H.152, E.161, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, E.247, G.267, G.268, Q.269, M.284, E.285, D.286, L.287, L.290 Chain C: R.233 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:E.149, A:W.151, A:W.151, A:V.240, A:V.244, A:L.245, A:L.245, A:M.284, A:L.287, A:L.290 Hydrogen bonds: A:R.145, A:E.198, A:E.198, A:E.198, A:I.199, A:E.247, A:Q.269, A:Q.269, C:R.233 Metal complexes: A:H.152, A:H.197 B12.5: 28 residues within 4Å: Chain B: L.144, R.145, G.148, E.149, W.151, H.152, E.161, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, E.247, G.267, G.268, Q.269, M.284, E.285, D.286, L.287, L.290 Chain D: R.233 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:E.149, B:W.151, B:W.151, 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.198, B:E.198, B:I.199, B:E.247, B:Q.269, B:Q.269, D:R.233 Metal complexes: B:H.152, B:H.197 B12.9: 28 residues within 4Å: Chain A: R.233 Chain C: L.144, R.145, G.148, E.149, W.151, H.152, E.161, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, E.247, G.267, G.268, Q.269, M.284, E.285, D.286, L.287, L.290 21 PLIP interactions: 1 interactions with chain A, 20 interactions with chain C, Hydrogen bonds: A:R.233, C:R.145, C:E.198, C:E.198, C:E.198, C:I.199, C:E.247, C:Q.269, C:Q.269 Hydrophobic interactions: C:E.149, C:W.151, C:W.151, C:V.240, C:V.244, C:L.245, C:L.245, C:M.284, C:L.287, C:L.290 Metal complexes: C:H.152, C:H.197 B12.13: 28 residues within 4Å: Chain B: R.233 Chain D: L.144, R.145, G.148, E.149, W.151, H.152, E.161, R.196, H.197, E.198, I.199, G.200, L.203, V.240, L.241, S.242, V.244, L.245, E.247, G.267, G.268, Q.269, M.284, E.285, D.286, L.287, L.290 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:E.149, D:W.151, D:W.151, D:V.240, D:V.244, D:L.245, D:L.245, D:M.284, D:L.287, D:L.290 Hydrogen bonds: D:R.145, D:E.198, D:E.198, D:I.199, D:E.247, D:Q.269, D:Q.269, B:R.233 Metal complexes: D:H.152, D:H.197

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: H.62, R.63 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.87 Chain B: A.88, R.91 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: H.62, R.63 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: A.88, R.91 Chain B: K.87 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: H.62, R.63 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: K.87 Chain D: A.88, R.91 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain D: H.62, R.63 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: A.88, R.91 Chain D: K.87 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: Q.173, D.177, R.209, L.216 Chain C: L.163, T.166, F.167, R.171 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:L.163, C:F.167, C:R.171, A:R.209, A:R.209 GOL.8: 8 residues within 4Å: Chain B: Q.173, D.177, R.209, L.216 Chain D: L.163, T.166, F.167, R.171 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:L.163, D:F.167, D:R.171, B:R.209, B:R.209 GOL.12: 8 residues within 4Å: Chain A: L.163, T.166, F.167, R.171 Chain C: Q.173, D.177, R.209, L.216 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:L.163, A:F.167, A:R.171, C:R.209, C:R.209 GOL.16: 8 residues within 4Å: Chain B: L.163, T.166, F.167, R.171 Chain D: Q.173, D.177, R.209, L.216 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:L.163, B:F.167, B:R.171, D:R.209, D:R.209

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
A

C
A

D
A

Light-dependent transcriptional regulator CarH

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