SMTL ID : 8c35.1

Dark state 2.1 Angstrom crystal structure of H132A variant of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 31 residues within 4Å: Chain A: L.44, L.47, R.48, G.51, E.52, W.54, E.64, H.65, S.68, G.97, E.98, R.99, H.100, E.101, I.102, G.103, L.106, V.143, L.144, S.145, V.147, L.148, L.169, G.170, G.171, Q.172, M.187, E.188, D.189, L.190 Ligands: 5AD.2 22 PLIP interactions: 22 interactions with chain A, Hydrophobic interactions: A:L.47, A:V.143, A:V.147, A:L.148, A:L.148, A:M.187, A:L.190 Hydrogen bonds: A:R.48, A:E.52, A:R.99, A:H.100, A:H.100, A:E.101, A:E.101, A:E.101, A:I.102, A:Q.172, A:Q.172, A:Q.172 Water bridges: A:R.72, A:R.99 Metal complexes: A:H.100 B12.3: 32 residues within 4Å: Chain B: L.44, L.47, R.48, G.51, E.52, W.54, A.55, E.64, H.65, S.68, R.72, G.97, E.98, R.99, H.100, E.101, I.102, G.103, L.106, V.143, L.144, S.145, V.147, L.148, G.170, G.171, Q.172, M.187, E.188, D.189, L.190 Ligands: 5AD.4 23 PLIP interactions: 22 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:R.99, B:V.143, B:V.147, B:L.148, B:M.187, B:L.190 Hydrogen bonds: B:E.52, B:R.72, B:R.99, B:H.100, B:H.100, B:E.101, B:E.101, B:I.102, B:Q.172, B:Q.172 Water bridges: B:R.48, B:E.52, B:V.147, B:S.149, A:R.72 Salt bridges: B:R.48 Metal complexes: B:H.100 B12.5: 29 residues within 4Å: Chain C: L.44, L.47, R.48, G.51, E.52, W.54, E.64, H.65, S.68, G.97, E.98, R.99, H.100, E.101, I.102, G.103, L.106, V.143, L.144, S.145, V.147, L.148, G.170, G.171, Q.172, M.187, D.189, L.190 Ligands: 5AD.6 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:V.143, C:V.147, C:L.148, C:L.148, C:M.187, C:L.190 Hydrogen bonds: C:R.48, C:E.52, C:R.72, C:G.97, C:R.99, C:H.100, C:E.101, C:E.101, C:I.102, C:Q.172, C:Q.172, C:Q.172 Water bridges: C:Q.172, C:Q.172 Salt bridges: C:R.48 Metal complexes: C:H.100 B12.7: 31 residues within 4Å: Chain D: L.44, L.47, R.48, G.51, E.52, W.54, E.64, H.65, S.68, R.72, G.97, E.98, R.99, H.100, E.101, I.102, G.103, L.106, V.143, L.144, S.145, V.147, L.148, G.170, G.171, Q.172, M.187, E.188, D.189, L.190 Ligands: 5AD.8 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:V.143, D:V.147, D:L.148, D:L.148, D:M.187, D:L.190 Hydrogen bonds: D:E.52, D:R.72, D:G.97, D:R.99, D:H.100, D:E.101, D:E.101, D:I.102, D:Q.172, D:Q.172 Water bridges: D:E.40, D:E.40, D:R.48, D:R.48, D:E.52, D:R.99, C:R.72 Salt bridges: D:R.48 Metal complexes: D:H.100

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

5AD.2: 8 residues within 4Å: Chain A: W.54, V.61, E.64, H.65, H.100 Chain B: D.124, P.126 Ligands: B12.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.61, A:E.64 Water bridges: A:R.99, A:R.99 5AD.4: 8 residues within 4Å: Chain A: D.124, P.126 Chain B: W.54, V.61, E.64, H.65, H.100 Ligands: B12.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.61, B:E.64 5AD.6: 7 residues within 4Å: Chain C: W.54, V.61, E.64, H.65 Chain D: D.124, P.126 Ligands: B12.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.61 5AD.8: 7 residues within 4Å: Chain C: D.124, P.126 Chain D: W.54, V.61, E.64, H.65 Ligands: B12.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poddar, H. et al., Redox driven B 12 -ligand switch drives CarH photoresponse. Nat Commun (2023)

Release Date

2023-08-16

Peptides

Probable transcriptional regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable transcriptional regulator

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