SMTL ID : 8c34.1

Aerobic light exposed 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-tetramer

Ligands

4 x B12: COBALAMIN(Non-covalent)

B12.1: 27 residues within 4Å: Chain A: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, S.68, H.100, G.103, L.106, V.143, L.144, S.145, V.147, L.148, S.149, L.169, G.170, G.171, Q.172, M.187, E.188, D.189, L.190 Ligands: PEG.2 25 PLIP interactions: 25 interactions with chain A, Hydrophobic interactions: A:R.48, A:W.54, A:E.64, A:L.106, A:V.143, A:M.187, A:L.190, A:L.190 Hydrogen bonds: A:R.48, A:R.48, A:E.52, A:S.68, A:S.68, A:H.100, A:S.149, A:S.149, A:G.171, A:Q.172, A:Q.172, A:Q.172 Water bridges: A:E.101, A:I.102, A:G.103, A:E.150 Salt bridges: A:R.48 B12.3: 24 residues within 4Å: Chain B: L.47, R.48, G.51, E.52, W.54, H.55, E.64, S.68, H.100, G.103, V.143, L.144, S.145, V.147, L.148, S.149, L.169, G.170, G.171, Q.172, M.187, E.188, D.189, L.190 30 PLIP interactions: 29 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.48, B:E.52, B:W.54, B:W.54, B:V.143, B:V.147, B:L.148, B:M.187, B:L.190 Hydrogen bonds: B:R.48, B:R.48, B:E.52, B:E.52, B:S.68, B:S.68, B:H.100, B:S.149, B:S.149, B:G.171, B:Q.172, B:Q.172, B:Q.172 Water bridges: B:E.150, B:E.150, B:R.153, B:R.153, B:G.171 Salt bridges: B:R.48 Metal complexes: B:H.55, H2O.11 B12.5: 24 residues within 4Å: Chain C: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, S.68, H.100, G.103, 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 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:W.54, C:W.54, C:E.64, C:V.143, C:L.148, C:M.187, C:L.190 Hydrogen bonds: C:E.52, C:E.64, C:E.64, C:S.68, C:H.100, C:G.171, C:Q.172, C:Q.172, C:Q.172, C:Q.172 Water bridges: C:R.48, C:R.48, C:E.101, C:I.102, C:L.190 B12.6: 24 residues within 4Å: Chain D: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, S.68, H.100, G.103, V.143, L.144, S.145, V.147, L.148, S.149, L.169, G.170, G.171, Q.172, M.187, E.188, L.190 25 PLIP interactions: 25 interactions with chain D, Hydrophobic interactions: D:W.54, D:W.54, D:E.64, D:V.143, D:V.147, D:L.148, D:M.187, D:L.190, D:L.190 Hydrogen bonds: D:E.52, D:E.64, D:S.68, D:S.149, D:S.149, D:G.171, D:Q.172, D:Q.172, D:Q.172 Water bridges: D:E.40, D:H.100, D:E.101, D:E.101, D:E.150, D:G.171 Metal complexes: D:H.55

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 7 residues within 4Å: Chain A: E.36, L.39, E.40, L.44, R.48, H.110 Ligands: B12.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40, A:R.48

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 8 residues within 4Å: Chain A: D.80, F.84, R.112 Chain B: A.20, E.23 Chain C: E.36, R.113, K.114 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.80, A:R.112, A:R.112, C:K.114 Water bridges: C:R.113

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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