SMTL ID : 5lcb.1

In situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy

Coordinates

PDB Format Compare

Method

SOLID-STATE NMR

Oligo State

homo-14-mer

Ligands

14 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 18 residues within 4Å: Chain A: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain B: L.36, T.40, I.43 Chain E: I.43 Chain J: I.10, L.11, A.14, I.17, F.18 Chain M: M.1 Ligands: BCL.10 12 PLIP interactions: 2 interactions with chain B, 5 interactions with chain J, 5 interactions with chain A, Hydrophobic interactions: B:T.40, B:I.43, J:L.11, J:F.18, J:F.18, J:F.18, A:W.26, A:W.26, A:V.29 pi-Stacking: J:F.18 pi-Cation interactions: A:H.25 Metal complexes: A:H.25 BCL.2: 18 residues within 4Å: Chain A: L.36, T.40, I.43 Chain B: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain H: I.43 Chain J: M.1 Chain M: I.10, L.11, A.14, I.17, F.18 Ligands: BCL.13 13 PLIP interactions: 6 interactions with chain B, 4 interactions with chain M, 2 interactions with chain A, 1 interactions with chain H, Hydrophobic interactions: B:F.18, B:W.26, B:W.26, B:V.29, M:L.11, M:F.18, M:F.18, A:L.36, A:T.40, H:I.43 pi-Cation interactions: B:H.25 Metal complexes: B:H.25 pi-Stacking: M:F.18 BCL.3: 10 residues within 4Å: Chain C: F.18, M.21, V.22, H.25, W.26, V.29 Chain G: M.1 Chain N: L.36, T.40, I.43 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:F.18, C:W.26, C:W.26, C:V.29 pi-Stacking: C:H.25 Metal complexes: C:H.25 BCL.4: 11 residues within 4Å: Chain D: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain F: M.1 Chain I: L.36, T.40, I.43 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain I, Hydrophobic interactions: D:F.18, D:W.26, D:W.26, D:V.29, I:L.36, I:I.43 pi-Cation interactions: D:H.25 Metal complexes: D:H.25 BCL.5: 10 residues within 4Å: Chain A: M.1 Chain E: F.18, M.21, V.22, H.25, W.26, V.29 Chain J: L.36, T.40, I.43 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain J, Hydrophobic interactions: E:F.18, E:W.26, E:W.26, E:V.29, J:L.36 pi-Stacking: E:H.25 pi-Cation interactions: E:H.25 Metal complexes: E:H.25 BCL.6: 17 residues within 4Å: Chain D: I.43 Chain F: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain I: I.10, L.11, A.14, I.17, F.18 Chain K: L.36, T.40, I.43 Ligands: BCL.9 14 PLIP interactions: 6 interactions with chain I, 6 interactions with chain F, 1 interactions with chain K, 1 interactions with chain D, Hydrophobic interactions: I:L.11, I:A.14, I:F.18, I:F.18, I:F.18, F:W.26, F:W.26, F:V.29, K:T.40, D:I.43 pi-Stacking: I:F.18, F:H.25 pi-Cation interactions: F:H.25 Metal complexes: F:H.25 BCL.7: 17 residues within 4Å: Chain C: I.43 Chain G: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain L: L.36, T.40, I.43 Chain N: I.10, L.11, A.14, I.17, F.18 Ligands: BCL.14 11 PLIP interactions: 5 interactions with chain G, 1 interactions with chain L, 5 interactions with chain N, Hydrophobic interactions: G:W.26, G:V.29, L:L.36, N:A.14, N:F.18, N:F.18, N:F.18 pi-Stacking: G:H.25, N:F.18 pi-Cation interactions: G:H.25 Metal complexes: G:H.25 BCL.8: 11 residues within 4Å: Chain B: M.1 Chain H: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain M: L.36, T.40, I.43 7 PLIP interactions: 6 interactions with chain H, 1 interactions with chain M, Hydrophobic interactions: H:F.18, H:W.26, H:W.26, H:V.29, M:L.36 pi-Cation interactions: H:H.25 Metal complexes: H:H.25 BCL.9: 17 residues within 4Å: Chain D: L.36, T.40, I.43 Chain F: I.10, L.11, A.14, I.17, F.18 Chain I: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain K: I.43 Ligands: BCL.6 12 PLIP interactions: 7 interactions with chain I, 1 interactions with chain K, 4 interactions with chain F, Hydrophobic interactions: I:W.26, I:W.26, I:V.29, K:I.43, F:F.18, F:F.18, F:F.18 pi-Stacking: I:H.25, F:F.18 pi-Cation interactions: I:H.25, I:H.25 Metal complexes: I:H.25 BCL.10: 17 residues within 4Å: Chain A: I.10, L.11, A.14, I.17, F.18 Chain B: I.43 Chain E: L.36, T.40, I.43 Chain J: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Ligands: BCL.1 14 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B, 2 interactions with chain E, 6 interactions with chain J, Hydrophobic interactions: A:L.11, A:F.18, A:F.18, A:F.18, B:I.43, E:L.36, E:T.40, J:W.26, J:W.26, J:V.29 pi-Stacking: A:F.18, J:H.25 pi-Cation interactions: J:H.25 Metal complexes: J:H.25 BCL.11: 11 residues within 4Å: Chain F: L.36, T.40, I.43 Chain I: M.1 Chain K: F.18, M.21, V.22, H.25, W.26, T.28, V.29 7 PLIP interactions: 6 interactions with chain K, 1 interactions with chain F, Hydrophobic interactions: K:F.18, K:W.26, K:W.26, K:V.29, F:L.36 pi-Cation interactions: K:H.25 Metal complexes: K:H.25 BCL.12: 11 residues within 4Å: Chain G: L.36, T.40, I.43 Chain L: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Chain N: M.1 7 PLIP interactions: 6 interactions with chain L, 1 interactions with chain G, Hydrophobic interactions: L:F.18, L:W.26, L:W.26, L:V.29, G:L.36 pi-Cation interactions: L:H.25 Metal complexes: L:H.25 BCL.13: 17 residues within 4Å: Chain A: I.43 Chain B: I.10, L.11, A.14, I.17, F.18 Chain H: L.36, T.40, I.43 Chain M: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Ligands: BCL.2 10 PLIP interactions: 5 interactions with chain M, 3 interactions with chain B, 1 interactions with chain H, 1 interactions with chain A, Hydrophobic interactions: M:W.26, M:W.26, M:V.29, B:A.14, B:F.18, B:F.18, H:L.36, A:I.43 pi-Cation interactions: M:H.25 Metal complexes: M:H.25 BCL.14: 17 residues within 4Å: Chain C: L.36, T.40, I.43 Chain G: I.10, L.11, A.14, I.17, F.18 Chain L: I.43 Chain N: F.18, M.21, V.22, H.25, W.26, T.28, V.29 Ligands: BCL.7 11 PLIP interactions: 6 interactions with chain N, 5 interactions with chain G, Hydrophobic interactions: N:F.18, N:W.26, N:W.26, N:V.29, G:L.11, G:A.14, G:F.18, G:F.18 pi-Cation interactions: N:H.25 Metal complexes: N:H.25 pi-Stacking: G:F.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nielsen, J.T. et al., In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum. Nat Commun (2016)

Release Date

2016-07-27

Peptides

Bacteriochlorophyll c-binding protein: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

Bacteriochlorophyll c-binding protein

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