SMTL ID : 3jqm.2 (1 other biounit)

Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC from Thermus theromophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 13 residues within 4Å: Chain A: V.47, K.49, D.126, K.129, A.130, K.133 Chain D: V.14, C.74, H.75, T.107, G.108, M.111 Ligands: FLC.17 17 PLIP interactions: 8 interactions with chain A, 9 interactions with chain D Water bridges: A:G.48, D:H.75, D:G.108, D:G.108, D:G.108, D:E.110 Salt bridges: A:K.49, A:K.49, A:K.49, A:K.129, A:K.129, A:K.129, A:K.133, D:H.75, D:H.75 Hydrogen bonds: D:H.75, D:G.108 GTP.6: 13 residues within 4Å: Chain B: V.47, G.48, K.49, D.126, K.129, A.130 Chain C: V.14, C.74, H.75, T.107, G.108, M.111 Ligands: FLC.11 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain C Water bridges: B:K.129, C:K.19, C:M.111 Salt bridges: B:K.49, B:K.49, B:K.49, B:K.129, B:K.129, B:K.129, C:H.75, C:H.75 Hydrogen bonds: C:H.75, C:G.108, C:G.108 GTP.10: 14 residues within 4Å: Chain B: V.14, C.74, H.75, T.107, G.108, M.111 Chain C: V.47, G.48, K.49, D.126, K.129, A.130, A.131 Ligands: FLC.7 14 PLIP interactions: 6 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:H.75, B:T.107, B:G.108 Water bridges: B:H.75, C:A.130, C:A.130 Salt bridges: B:H.75, B:H.75, C:K.49, C:K.49, C:K.49, C:K.129, C:K.129, C:K.129 GTP.16: 14 residues within 4Å: Chain A: V.14, L.73, C.74, H.75, T.107, M.111 Chain D: V.47, G.48, K.49, D.126, K.129, A.130, A.131 Ligands: FLC.2 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:H.75, A:T.107, D:A.130 Water bridges: A:H.75, A:G.108, A:G.108, A:E.110 Salt bridges: A:H.75, A:H.75, D:K.49, D:K.49, D:K.49, D:K.129, D:K.129, D:K.129 GTP.22: 12 residues within 4Å: Chain E: V.47, K.49, D.126, K.129, A.130 Chain F: V.14, C.74, H.75, T.107, G.108, M.111 Ligands: FLC.29 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain E Hydrogen bonds: F:H.75, F:G.108 Water bridges: F:H.75, F:G.108 Salt bridges: F:H.75, F:H.75, E:K.49, E:K.49, E:K.49, E:K.129, E:K.129, E:K.129 GTP.28: 10 residues within 4Å: Chain E: V.14, C.74, H.75, T.107 Chain F: V.47, G.48, K.49, D.126, K.129, A.130 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:H.75, E:T.107 Salt bridges: E:H.75, E:H.75, F:K.49, F:K.49, F:K.49, F:K.129, F:K.129, F:K.129

6 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 12 residues within 4Å: Chain A: K.19, R.24, E.106, T.107, G.108, E.110, K.145, G.148, K.149, S.150 Chain D: K.133 Ligands: GTP.16 15 PLIP interactions: 3 interactions with chain D, 12 interactions with chain A Hydrogen bonds: D:K.133, A:E.106, A:G.108, A:K.149, A:S.150, A:S.150, A:S.150 Salt bridges: D:K.129, D:K.133, A:K.19, A:K.19, A:R.24, A:R.24, A:K.145, A:K.149 FLC.7: 14 residues within 4Å: Chain B: K.19, R.24, E.106, T.107, G.108, E.110, K.145, G.147, G.148, K.149, S.150 Chain C: K.129, K.133 Ligands: GTP.10 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:K.149 Hydrogen bonds: B:R.24, B:G.108, B:E.110, B:K.145, B:K.145, B:K.149, B:S.150, B:S.150 Salt bridges: B:K.19, B:K.19, B:R.24, B:K.145, C:K.129, C:K.133 FLC.11: 11 residues within 4Å: Chain B: K.129, A.130, K.133 Chain C: R.24, E.110, K.145, G.147, G.148, K.149, S.150 Ligands: GTP.6 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Salt bridges: B:K.129, B:K.133, B:K.133, B:K.133, C:R.24, C:K.145 Hydrogen bonds: C:K.149, C:S.150, C:S.150 FLC.17: 10 residues within 4Å: Chain A: K.133 Chain D: K.19, R.24, G.108, E.110, K.145, G.148, K.149, S.150 Ligands: GTP.1 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:K.145, D:K.149, D:S.150, D:S.150, D:S.150, D:S.150 Water bridges: D:K.19, D:K.19, D:G.108 Salt bridges: D:K.19, D:R.24, D:R.24, D:K.145, D:K.145, A:K.129, A:K.133, A:K.133 FLC.23: 8 residues within 4Å: Chain E: R.24, G.108, E.110, K.145, G.148, K.149, S.150 Chain F: K.133 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:K.145, E:K.145, E:K.149, E:S.150, E:S.150 Salt bridges: E:K.19, E:R.24, E:R.24, E:K.145, E:K.145, F:K.129, F:K.133, F:K.133 FLC.29: 10 residues within 4Å: Chain F: K.19, R.24, E.106, T.107, G.108, K.145, G.147, K.149, S.150 Ligands: GTP.22 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.24, F:T.107, F:G.108, F:K.145, F:G.147, F:K.149, F:S.150 Salt bridges: F:K.19, F:K.19, F:R.24, F:K.145, F:K.145, E:K.129

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.83, R.85 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.85 Water bridges: A:R.85 GOL.12: 4 residues within 4Å: Chain C: L.88, L.89, K.90, A.91 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.90, C:K.90, C:K.90, C:A.91 GOL.24: 6 residues within 4Å: Chain A: R.10 Chain E: L.53, V.54, Q.57, R.85, V.86 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:L.53, E:V.84, E:V.86

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

EDO.4: 6 residues within 4Å: Chain A: E.83, R.85, E.98, A.99, T.100 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83, A:T.100 EDO.8: 4 residues within 4Å: Chain B: E.83, E.98, A.99, T.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.99, B:T.100 EDO.9: 7 residues within 4Å: Chain A: L.77 Chain B: P.78 Chain E: P.76, L.77, P.78 Ligands: PEG.5, PEG.27 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:L.77, E:P.76 EDO.13: 5 residues within 4Å: Chain C: E.83, R.85, E.98, A.99, T.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.83, C:T.100 EDO.14: 3 residues within 4Å: Chain C: L.42, G.45, D.51 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.42 EDO.18: 4 residues within 4Å: Chain D: E.83, R.85, E.98, T.100 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.85, D:T.100, D:T.100 EDO.19: 8 residues within 4Å: Chain D: A.64, K.65, K.66, T.67, A.68, P.76, L.77, E.112 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.68, D:L.77, D:L.77 EDO.20: 2 residues within 4Å: Chain D: R.141, R.155 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.155 Water bridges: D:R.141 EDO.21: 3 residues within 4Å: Chain D: K.66, D.69 Chain F: D.69 No protein-ligand interaction detected (PLIP) EDO.25: 6 residues within 4Å: Chain A: R.10 Chain E: E.83, R.85, E.98, A.99, T.100 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:E.98, E:A.99, E:T.100, A:R.10, A:R.10 EDO.26: 4 residues within 4Å: Chain E: L.42, D.51, P.52, L.53 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.51 EDO.30: 4 residues within 4Å: Chain F: E.83, E.98, A.99, T.100 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:E.83, F:E.98 Water bridges: C:R.12 EDO.31: 4 residues within 4Å: Chain F: L.42, G.45, D.51, L.53 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.51

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

PEG.5: 9 residues within 4Å: Chain A: A.64, K.65, A.68, P.76, L.77, L.79, E.112 Ligands: EDO.9, PEG.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.77, A:E.112 PEG.15: 5 residues within 4Å: Chain C: L.77, P.78 Chain D: P.76, L.77, P.78 No protein-ligand interaction detected (PLIP) PEG.27: 9 residues within 4Å: Chain E: A.64, K.65, T.67, A.68, P.76, L.77, E.112 Ligands: PEG.5, EDO.9 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.67, E:A.68, E:L.77, E:E.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanaujia, S.P. et al., Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-06-30

Peptides

Molybdenum cofactor biosynthesis protein C: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
F

D
G

E
H

F
I

Molybdenum cofactor biosynthesis protein C

Related Entries With Identical Sequence