SMTL ID : 8c31.1

Dark state 1.8 Angstrom crystal structure of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

3 x BR: BROMIDE ION(Non-covalent)

BR.1: 2 residues within 4Å: Chain A: R.72, Q.76 Ligand excluded by PLIP BR.5: 3 residues within 4Å: Chain B: A.82, Y.109, R.113 Ligand excluded by PLIP BR.8: 1 residues within 4Å: Chain C: Q.76 Ligand excluded by PLIP

4 x B12: COBALAMIN(Non-covalent)

B12.2: 31 residues within 4Å: Chain A: L.44, L.47, R.48, G.51, E.52, W.54, H.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, D.189, L.190 Ligands: 5AD.3 24 PLIP interactions: 23 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:L.47, A:I.102, A:L.106, A:V.143, A:V.147, A:L.148, A:L.148, A:M.187, A:L.190 Hydrogen bonds: A:R.72, A:R.99, A:H.100, A:H.100, A:E.101, A:E.101, A:I.102, A:Q.172, A:Q.172 Water bridges: A:R.48, A:R.48, A:R.48, A:R.99, B:R.72 Metal complexes: A:H.100 B12.6: 30 residues within 4Å: Chain B: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, H.65, S.68, G.97, E.98, R.99, H.100, E.101, I.102, G.103, 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.7 22 PLIP interactions: 22 interactions with chain B, Hydrophobic interactions: B:L.44, B:L.47, B:W.54, B:V.143, B:V.147, B:L.148, B:M.187, B:L.190 Hydrogen bonds: B:E.52, B:R.72, B:G.97, B:R.99, B:H.100, B:E.101, B:I.102, B:Q.172, B:Q.172 Water bridges: B:R.48, B:E.150, B:E.150 Salt bridges: B:R.48 Metal complexes: B:H.100 B12.9: 32 residues within 4Å: Chain C: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, H.65, S.68, R.72, G.97, E.98, R.99, H.100, E.101, I.102, G.103, 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.10, PGE.12 23 PLIP interactions: 22 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:L.47, 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:Q.172, C:Q.172 Water bridges: C:R.48, C:R.48, C:I.102, C:I.102, D:R.72 Salt bridges: C:R.48 Metal complexes: C:H.100 B12.15: 30 residues within 4Å: Chain D: L.44, L.47, R.48, G.51, E.52, W.54, H.55, E.64, H.65, S.68, R.72, G.97, E.98, R.99, H.100, E.101, I.102, G.103, V.143, L.144, S.145, V.147, L.148, G.170, G.171, Q.172, M.187, D.189, L.190 Ligands: 5AD.16 28 PLIP interactions: 27 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:L.44, D:L.47, D:V.143, D:V.147, D:L.148, D:L.148, D:M.187, D:L.190 Hydrogen bonds: D:E.52, D:H.55, 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:R.48, D:E.52, D:R.99, D:V.147, D:S.149, D:E.150, C:R.72 Salt bridges: D:R.48 Metal complexes: D:H.100

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

5AD.3: 7 residues within 4Å: Chain A: W.54, V.61, E.64, H.65 Chain B: D.124, P.126 Ligands: B12.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.61, A:E.64 Water bridges: A:R.99, A:R.99, B:D.124 5AD.7: 7 residues within 4Å: Chain A: D.124, P.126 Chain B: W.54, V.61, E.64, H.65 Ligands: B12.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.61, B:E.64 Water bridges: B:R.99 5AD.10: 8 residues within 4Å: Chain C: W.54, V.61, E.64, H.65, H.100 Chain D: D.124, P.126 Ligands: B12.9 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.61 5AD.16: 7 residues within 4Å: Chain C: D.124, P.126 Chain D: W.54, V.61, E.64, H.65 Ligands: B12.15 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.61 Water bridges: D:R.99, D:R.99, D:R.99

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 2 residues within 4Å: Chain A: W.54, H.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.55 IMD.11: 2 residues within 4Å: Chain C: P.156, D.157 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.157

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

PGE.12: 4 residues within 4Å: Chain C: R.99, L.148, E.150 Ligands: B12.9 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.99

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain C: A.132 Chain D: G.60 2 PLIP interactions: 2 interactions with chain D Water bridges: D:G.60, D:G.60 EDO.14: 7 residues within 4Å: Chain C: Q.76, L.79, D.80, R.112 Chain D: T.69, F.70, A.73 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.76, C:R.112, C:R.112 Water bridges: D:F.70 EDO.17: 2 residues within 4Å: Chain D: W.54, H.55 2 PLIP interactions: 2 interactions with chain D Water bridges: D:W.54, D:G.57 EDO.18: 7 residues within 4Å: Chain D: D.162, A.164, P.165, R.166, V.167, G.183, E.185 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.162, D:V.167, D:G.183, D:E.185, D:E.185 EDO.19: 1 residues within 4Å: Chain D: L.127 No protein-ligand interaction detected (PLIP)

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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