SMTL ID : 7alq.2 (1 other biounit)

human GCH-GFRP inhibitory complex 7-deaza-GTP bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-10-10-mer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.100, H.103, C.171 Ligands: QBQ.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.100, A:H.103, A:C.171 ZN.4: 4 residues within 4Å: Chain B: C.100, H.103, C.171 Ligands: QBQ.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.100, B:H.103, B:C.171 ZN.8: 4 residues within 4Å: Chain C: C.100, H.103, C.171 Ligands: QBQ.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.100, C:H.103, C:C.171 ZN.11: 5 residues within 4Å: Chain D: C.100, H.102, H.103, C.171 Ligands: QBQ.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.100, D:H.103, D:C.171 ZN.13: 4 residues within 4Å: Chain E: C.100, H.103, C.171 Ligands: QBQ.2 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.100, E:H.103, E:C.171 ZN.16: 4 residues within 4Å: Chain F: C.100, H.103, C.171 Ligands: QBQ.20 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.100, F:H.103, F:C.171 ZN.19: 4 residues within 4Å: Chain G: C.100, H.103, C.171 Ligands: QBQ.23 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.100, G:H.103, G:C.171 ZN.22: 5 residues within 4Å: Chain H: C.100, H.102, H.103, C.171 Ligands: QBQ.26 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.100, H:H.103, H:C.171 ZN.25: 4 residues within 4Å: Chain I: C.100, H.103, C.171 Ligands: QBQ.29 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.100, I:H.103, I:C.171 ZN.28: 5 residues within 4Å: Chain J: C.100, H.102, H.103, C.171 Ligands: QBQ.17 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.100, J:H.103, J:C.171

10 x QBQ: 7-deaza-GTP(Non-covalent)

QBQ.2: 21 residues within 4Å: Chain A: N.77, A.79, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain E: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain F: R.56 Ligands: ZN.13 23 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F, 9 interactions with chain E Hydrophobic interactions: A:L.124 Hydrogen bonds: A:N.77, A:L.122, A:L.124, A:S.125, A:S.125, A:S.125, A:K.126, E:Q.141 Water bridges: A:L.122, E:R.175, E:R.175, E:R.175 Salt bridges: A:K.126, A:K.126, A:K.126, A:R.129, F:R.56, E:H.103, E:E.142, E:R.175, E:R.175 pi-Stacking: E:H.102 QBQ.5: 22 residues within 4Å: Chain A: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain B: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: R.56 Ligands: ZN.1 23 PLIP interactions: 8 interactions with chain A, 13 interactions with chain B, 2 interactions with chain J Hydrogen bonds: A:Q.141, B:N.77, B:L.122, B:L.124, B:S.125, B:S.125, B:S.125, B:K.126 Water bridges: A:R.175, B:R.129, J:R.56 Salt bridges: A:H.103, A:H.103, A:E.142, A:R.175, A:R.175, B:K.126, B:K.126, B:K.126, B:R.129, J:R.56 pi-Cation interactions: A:H.102 Hydrophobic interactions: B:L.124 QBQ.9: 22 residues within 4Å: Chain B: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain C: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain I: R.56 Ligands: ZN.4 24 PLIP interactions: 10 interactions with chain B, 13 interactions with chain C, 1 interactions with chain I Hydrogen bonds: B:Q.141, C:N.77, C:L.122, C:L.124, C:S.125, C:S.125, C:S.125, C:K.126 Water bridges: B:R.175, B:R.175, B:V.177, C:L.122 Salt bridges: B:H.103, B:H.103, B:E.142, B:R.175, B:R.175, C:K.126, C:K.126, C:K.126, C:R.129, I:R.56 pi-Cation interactions: B:H.102 Hydrophobic interactions: C:L.124 QBQ.12: 22 residues within 4Å: Chain C: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain D: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain H: R.56 Ligands: ZN.8 27 PLIP interactions: 11 interactions with chain C, 14 interactions with chain D, 2 interactions with chain H Hydrogen bonds: C:Q.141, D:N.77, D:L.122, D:L.124, D:S.125, D:S.125, D:K.126, D:K.126, D:K.126 Water bridges: C:H.103, C:R.175, C:R.175, C:R.175, D:R.129, D:R.129 Salt bridges: C:H.103, C:H.103, C:E.142, C:R.175, C:R.175, D:K.126, D:K.126, D:K.126, D:R.129, H:K.52, H:R.56 pi-Cation interactions: C:H.102 QBQ.14: 22 residues within 4Å: Chain D: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain E: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain G: R.56 Ligands: ZN.11 27 PLIP interactions: 13 interactions with chain E, 11 interactions with chain D, 3 interactions with chain G Hydrophobic interactions: E:L.124 Hydrogen bonds: E:N.77, E:L.122, E:L.124, E:S.125, E:S.125, E:S.125, E:K.126, D:Q.141 Water bridges: E:L.122, D:R.175, D:R.175, D:R.175, D:V.177, G:K.52 Salt bridges: E:K.126, E:K.126, E:K.126, E:R.129, D:H.103, D:H.103, D:E.142, D:R.175, D:R.175, G:K.52, G:R.56 pi-Cation interactions: D:H.102 QBQ.17: 23 residues within 4Å: Chain A: K.52, R.56 Chain F: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Chain J: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Ligands: ZN.28 23 PLIP interactions: 9 interactions with chain J, 11 interactions with chain F, 3 interactions with chain A Hydrogen bonds: J:Q.141, F:N.77, F:L.122, F:L.124, F:S.125, F:S.125, F:K.126 Water bridges: J:H.103, J:R.175, A:K.52 Salt bridges: J:H.103, J:H.103, J:E.142, J:R.175, J:R.175, F:K.126, F:K.126, F:K.126, F:R.129, A:K.52, A:R.56 pi-Stacking: J:H.102 Hydrophobic interactions: F:L.124 QBQ.20: 22 residues within 4Å: Chain E: K.52, R.56 Chain F: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175 Chain G: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.16 26 PLIP interactions: 15 interactions with chain G, 9 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: G:L.124 Hydrogen bonds: G:N.77, G:L.122, G:L.124, G:S.125, G:S.125, G:S.125, G:S.125, G:K.126, G:K.126, F:Q.141 Water bridges: G:R.129, F:R.175, F:R.175 Salt bridges: G:K.126, G:K.126, G:K.126, G:R.129, F:H.103, F:H.103, F:E.142, F:R.175, F:R.175, E:K.52, E:R.56 pi-Stacking: F:H.102 QBQ.23: 21 residues within 4Å: Chain D: R.56 Chain G: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain H: N.77, A.79, F.81, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.19 27 PLIP interactions: 13 interactions with chain G, 13 interactions with chain H, 1 interactions with chain D Hydrogen bonds: G:Q.141, H:N.77, H:L.122, H:L.124, H:S.125, H:S.125, H:K.126, H:K.126, H:K.126 Water bridges: G:H.103, G:R.175, G:R.175, G:R.175, G:R.175, G:V.177 Salt bridges: G:H.103, G:H.103, G:E.142, G:R.175, G:R.175, H:K.126, H:K.126, H:K.126, H:R.129, D:R.56 pi-Stacking: G:H.102 Hydrophobic interactions: H:L.124 QBQ.26: 23 residues within 4Å: Chain C: K.52, R.56 Chain H: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain I: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.22 25 PLIP interactions: 14 interactions with chain I, 9 interactions with chain H, 2 interactions with chain C Hydrophobic interactions: I:L.124 Hydrogen bonds: I:N.77, I:L.122, I:L.124, I:S.125, I:S.125, I:S.125, I:K.126, H:Q.141 Water bridges: I:L.122, I:R.129, H:H.103, H:R.175 Salt bridges: I:K.126, I:K.126, I:K.126, I:R.129, H:H.103, H:H.103, H:E.142, H:R.175, H:R.175, C:K.52, C:R.56 pi-Cation interactions: H:H.102 QBQ.29: 22 residues within 4Å: Chain B: R.56 Chain I: C.100, H.102, H.103, V.140, Q.141, E.142, H.169, C.171, R.175, G.176 Chain J: N.77, A.79, F.81, V.121, L.122, G.123, L.124, S.125, K.126, R.129 Ligands: ZN.25 25 PLIP interactions: 10 interactions with chain I, 14 interactions with chain J, 1 interactions with chain B Hydrogen bonds: I:Q.141, J:N.77, J:L.122, J:L.124, J:S.125, J:S.125, J:S.125, J:S.125, J:K.126 Water bridges: I:R.175, I:R.175, I:V.177, J:L.122 Salt bridges: I:H.103, I:H.103, I:E.142, I:R.175, I:R.175, J:K.126, J:K.126, J:K.126, J:R.129, B:R.56 pi-Stacking: I:H.102 Hydrophobic interactions: J:L.124

10 x HBI: 7,8-DIHYDROBIOPTERIN(Non-covalent)

HBI.3: 13 residues within 4Å: Chain A: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 Chain E: S.187, T.188, M.189, R.194, R.200 13 PLIP interactions: 5 interactions with chain E, 8 interactions with chain A Hydrogen bonds: E:S.187, E:M.189, E:R.200, E:R.200, A:D.86, A:M.88 Water bridges: E:R.194, A:T.199, A:T.199 Hydrophobic interactions: A:L.116, A:A.159, A:V.192 Salt bridges: A:E.202 HBI.6: 13 residues within 4Å: Chain A: S.187, T.188, M.189, R.194, R.200 Chain B: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 12 PLIP interactions: 1 interactions with chain K, 5 interactions with chain A, 6 interactions with chain B Water bridges: K:Q.12, A:M.189, A:M.189 Hydrogen bonds: A:S.187, A:R.200, A:R.200, B:D.86, B:M.88 Hydrophobic interactions: B:L.116, B:A.159, B:V.192 Salt bridges: B:E.202 HBI.7: 13 residues within 4Å: Chain B: S.187, T.188, M.189, R.194, R.200 Chain C: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:S.187, B:R.200, B:R.200, C:D.86, C:M.88 Water bridges: B:R.194, B:R.194 Hydrophobic interactions: C:L.116, C:A.159, C:V.192 Salt bridges: C:E.202 HBI.10: 13 residues within 4Å: Chain C: S.187, T.188, M.189, R.194, R.200 Chain D: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.187, C:R.200, C:R.200, D:D.86, D:M.88 Water bridges: C:M.189, C:M.189, D:D.86, D:T.199, D:T.199 Hydrophobic interactions: D:L.116, D:A.159, D:V.192 Salt bridges: D:E.202 HBI.15: 13 residues within 4Å: Chain D: S.187, T.188, M.189, R.194, R.200 Chain E: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 13 PLIP interactions: 5 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:S.187, D:R.200, D:R.200, E:D.86, E:M.88 Water bridges: D:R.194, D:R.194, E:T.199, E:T.199 Hydrophobic interactions: E:L.116, E:A.159, E:V.192 Salt bridges: E:E.202 HBI.18: 13 residues within 4Å: Chain F: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 Chain J: S.187, T.188, M.189, R.194, R.200 14 PLIP interactions: 8 interactions with chain F, 6 interactions with chain J Hydrophobic interactions: F:L.116, F:A.159, F:V.192 Hydrogen bonds: F:D.86, F:M.88, J:S.187, J:R.200, J:R.200 Water bridges: F:T.199, F:T.199, J:M.189, J:M.189 Salt bridges: F:E.202 pi-Cation interactions: J:R.194 HBI.21: 13 residues within 4Å: Chain F: S.187, T.188, M.189, R.194, R.200 Chain G: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 14 PLIP interactions: 8 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:L.116, G:A.159, G:V.192 Hydrogen bonds: G:D.86, G:M.88, F:S.187, F:R.200, F:R.200 Water bridges: G:T.199, G:T.199, F:R.194, F:R.194 Salt bridges: G:E.202 pi-Cation interactions: F:R.194 HBI.24: 13 residues within 4Å: Chain G: S.187, T.188, M.189, R.194, R.200 Chain H: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 11 PLIP interactions: 6 interactions with chain H, 5 interactions with chain G Hydrophobic interactions: H:L.116, H:A.159, H:V.192 Hydrogen bonds: H:D.86, H:M.88, G:S.187, G:R.200, G:R.200 Salt bridges: H:E.202 Water bridges: G:M.189, G:M.189 HBI.27: 13 residues within 4Å: Chain H: S.187, T.188, M.189, R.194, R.200 Chain I: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 11 PLIP interactions: 6 interactions with chain I, 5 interactions with chain H Hydrophobic interactions: I:L.116, I:A.159, I:V.192 Hydrogen bonds: I:D.86, I:M.88, H:S.187, H:R.200, H:R.200 Salt bridges: I:E.202 Water bridges: H:M.189, H:M.189 HBI.30: 13 residues within 4Å: Chain I: S.187, T.188, M.189, R.194, R.200 Chain J: D.86, E.87, M.88, L.116, A.159, V.192, T.199, E.202 13 PLIP interactions: 7 interactions with chain J, 1 interactions with chain S, 5 interactions with chain I Hydrophobic interactions: J:L.116, J:A.159, J:V.192 Hydrogen bonds: J:D.86, J:M.88, I:S.187, I:R.200, I:R.200 Water bridges: J:D.196, S:Q.12, I:R.194, I:R.194 Salt bridges: J:E.202

10 x K: POTASSIUM ION(Non-covalent)

K.31: 4 residues within 4Å: Chain K: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:T.11, K:Q.12, K:R.14, K:V.17 K.32: 4 residues within 4Å: Chain L: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:T.11, L:Q.12, L:R.14, L:V.17 K.33: 5 residues within 4Å: Chain M: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:T.11, M:Q.12, M:R.14, M:V.17 K.34: 4 residues within 4Å: Chain N: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:T.11, N:Q.12, N:R.14, N:V.17 K.35: 5 residues within 4Å: Chain O: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:T.11, O:Q.12, O:R.14, O:V.17 K.36: 5 residues within 4Å: Chain P: T.11, Q.12, R.14, V.17, G.18 3 PLIP interactions: 3 interactions with chain P Metal complexes: P:Q.12, P:R.14, P:V.17 K.37: 4 residues within 4Å: Chain Q: T.11, Q.12, R.14, V.17 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:T.11, Q:Q.12, Q:R.14, Q:V.17 K.38: 4 residues within 4Å: Chain R: T.11, Q.12, R.14, V.17 5 PLIP interactions: 4 interactions with chain R, 1 Ligand-Water interactions Metal complexes: R:T.11, R:Q.12, R:R.14, R:V.17, H2O.38 K.39: 5 residues within 4Å: Chain S: T.11, Q.12, R.14, V.17, G.18 3 PLIP interactions: 3 interactions with chain S Metal complexes: S:Q.12, S:R.14, S:V.17 K.40: 5 residues within 4Å: Chain T: T.11, Q.12, R.14, V.17, G.18 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:T.11, T:Q.12, T:R.14, T:V.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ebenhoch, R. et al., Biophysical and structural investigation of the regulation of human GTP cyclohydrolase I by its regulatory protein GFRP. J.Struct.Biol. (2021)

Release Date

2021-10-20

Peptides

GTP cyclohydrolase 1: ABCDEFGHIJ
GTP cyclohydrolase 1 feedback regulatory protein: KLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
P

G
Q

H
R

I
S

J
T

K
k

L
l

M
m

N
n

O
o

P
p

Q
q

R
r

S
s

T
t

GTP cyclohydrolase 1

GTP cyclohydrolase 1 feedback regulatory protein

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