SMTL ID : 4rb4.1

Crystal structure of dodecameric iron-containing heptosyltransferase TibC in complex with ADP-D-beta-D-heptose at 3.9 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.88 Å

Oligo State

homo-12-mer

Ligands

12 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: C.339, C.342, C.358, C.370 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.339, A:C.342, A:C.358 FE.3: 4 residues within 4Å: Chain B: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.339, B:C.342, B:C.358, B:C.370 FE.5: 4 residues within 4Å: Chain C: C.339, C.342, C.358, C.370 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.339, C:C.342, C:C.370 FE.8: 4 residues within 4Å: Chain D: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.339, D:C.342, D:C.358, D:C.370 FE.10: 4 residues within 4Å: Chain E: C.339, C.342, C.358, C.370 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.342, E:C.358 FE.12: 4 residues within 4Å: Chain F: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.339, F:C.342, F:C.358, F:C.370 FE.14: 4 residues within 4Å: Chain G: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.339, G:C.342, G:C.358, G:C.370 FE.16: 4 residues within 4Å: Chain H: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.339, H:C.342, H:C.358, H:C.370 FE.18: 4 residues within 4Å: Chain I: C.339, C.342, C.358, C.370 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.339, I:C.342, I:C.370 FE.20: 4 residues within 4Å: Chain J: C.339, C.342, C.358, C.370 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.342, J:C.358, J:C.370 FE.23: 4 residues within 4Å: Chain K: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.339, K:C.342, K:C.358, K:C.370 FE.26: 4 residues within 4Å: Chain L: C.339, C.342, C.358, C.370 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.339, L:C.342, L:C.358, L:C.370

12 x AQH: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R,5R,6S)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate(Covalent)(Non-covalent)

AQH.2: 23 residues within 4Å: Chain A: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, S.321, E.326 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.107, A:L.108, A:G.109, A:G.109, A:T.226, A:K.230, A:D.256, A:D.256, A:R.257, A:R.257, A:D.258, A:L.281, A:R.286, A:S.301, A:G.302, A:S.321, A:E.326 Salt bridges: A:K.230, A:K.230 AQH.4: 20 residues within 4Å: Chain B: G.106, T.107, L.108, G.109, F.187, Q.224, S.225, T.226, I.255, D.256, R.257, G.279, K.280, L.281, R.286, P.300, S.301, G.302, L.303, W.305 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.256, B:D.256, B:L.281, B:R.286, B:G.302 AQH.7: 22 residues within 4Å: Chain C: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, E.326, W.343 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:T.107, C:T.107, C:L.108, C:G.109, C:T.226, C:T.226, C:K.230, C:D.256, C:R.257, C:R.257, C:L.281, C:R.286, C:G.302, C:W.305, C:E.326 Salt bridges: C:K.230, C:K.230 AQH.9: 21 residues within 4Å: Chain D: T.107, L.108, G.109, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, E.326, W.343 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:K.230, D:D.256, D:R.257, D:L.281, D:R.286, D:G.302, D:E.326 Salt bridges: D:K.230, D:K.230 AQH.11: 22 residues within 4Å: Chain E: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, F.320, E.326, W.343 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:T.107, E:T.107, E:L.108, E:G.109, E:T.226, E:T.226, E:T.226, E:D.256, E:R.257, E:R.257, E:L.281, E:R.286, E:G.302, E:W.343 Salt bridges: E:K.230, E:K.230 AQH.13: 21 residues within 4Å: Chain F: L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, E.326, W.343 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:L.108, F:L.108, F:T.226, F:T.226, F:K.230, F:D.256, F:L.281, F:R.286, F:G.302, F:W.343 Salt bridges: F:K.230, F:K.230 AQH.15: 23 residues within 4Å: Chain G: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, S.321, E.326 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:T.107, G:L.108, G:G.109, G:A.110, G:T.226, G:T.226, G:K.230, G:R.257, G:R.257, G:D.258, G:L.281, G:R.286, G:P.300, G:G.302, G:S.321, G:E.326, G:E.326 Salt bridges: G:K.230, G:K.230 AQH.17: 20 residues within 4Å: Chain H: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, E.326 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:L.108, H:G.109, H:A.110, H:T.226, H:T.226, H:T.226, H:D.256, H:D.256, H:R.257, H:R.257, H:L.281, H:R.286, H:G.302, H:E.326 Salt bridges: H:K.230, H:K.230 AQH.19: 22 residues within 4Å: Chain I: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, F.320, E.326, W.343 12 PLIP interactions: 12 interactions with chain I Hydrogen bonds: I:T.107, I:T.107, I:L.108, I:T.226, I:D.256, I:R.257, I:L.281, I:R.286, I:G.302, I:E.326 Salt bridges: I:K.230, I:K.230 AQH.22: 22 residues within 4Å: Chain J: T.107, L.108, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, I.255, D.256, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, E.326 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:T.107, J:T.107, J:T.107, J:L.108, J:G.109, J:T.226, J:T.226, J:T.226, J:K.230, J:D.256, J:D.256, J:R.257, J:L.281, J:R.286, J:G.302, J:W.305, J:E.326, J:E.326 Salt bridges: J:K.230, J:K.230 AQH.25: 19 residues within 4Å: Chain K: T.107, L.108, G.109, A.110, F.187, T.226, K.230, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, E.326, W.343 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:T.107, K:L.108, K:G.109, K:T.226, K:R.257, K:L.281, K:R.286, K:G.302, K:W.305, K:S.325, K:E.326, K:E.326, K:W.343 Salt bridges: K:K.230, K:K.230 AQH.27: 20 residues within 4Å: Chain L: T.107, G.109, A.110, F.187, Q.224, S.225, T.226, K.230, R.257, L.281, L.283, R.286, P.300, S.301, G.302, L.303, W.305, F.320, E.326, W.343 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:G.109, L:T.226, L:T.226, L:K.230, L:R.257, L:R.257, L:L.281, L:L.281, L:R.286, L:G.302, L:S.325, L:S.325 Salt bridges: L:K.230, L:K.230

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

EDO.6: 3 residues within 4Å: Chain C: R.189, R.200, E.201 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.189, C:R.189, C:E.201 EDO.21: 3 residues within 4Å: Chain J: R.189, R.200, E.201 No protein-ligand interaction detected (PLIP) EDO.24: 3 residues within 4Å: Chain K: R.189, R.200, E.201 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:R.189, K:E.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, Q. et al., A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family. Elife (2014)

Release Date

2014-11-05

Peptides

Glycosyltransferase tibC: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
C

D
D

E
E

F
H

G
B

H
F

I
G

J
I

K
J

L
A

Glycosyltransferase tibC