SMTL ID : 2r50.3 (2 other biounits)

The crystal structure of nonsymbiotic corn hemoglobin 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 20 residues within 4Å: Chain A: M.53, F.54, K.69, H.73, V.77, M.80, T.99, R.103, L.104, T.107, H.108, Y.111, V.113, H.117, F.118, T.121, Y.150, L.153, V.154, I.157 23 PLIP interactions: 23 interactions with chain A, Hydrophobic interactions: A:F.54, A:V.77, A:L.104, A:T.107, A:Y.111, A:Y.111, A:V.113, A:F.118, A:F.118, A:Y.150, A:V.154, A:I.157 Hydrogen bonds: A:T.107, A:T.107 Water bridges: A:Y.111, A:Y.111 Salt bridges: A:K.69, A:R.103 pi-Stacking: A:H.73, A:H.108, A:H.108 Metal complexes: A:H.73, A:H.108 HEM.3: 19 residues within 4Å: Chain B: M.53, F.54, K.69, H.73, V.77, M.80, R.103, L.104, T.107, H.108, Y.111, V.113, H.117, F.118, T.121, Y.150, L.153, V.154, I.157 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:F.54, B:F.54, B:V.77, B:L.104, B:T.107, B:Y.111, B:Y.111, B:V.113, B:V.113, B:F.118, B:F.118, B:Y.150, B:L.153, B:V.154, B:I.157 Hydrogen bonds: B:T.107 Salt bridges: B:R.103 pi-Stacking: B:H.73, B:H.108 Metal complexes: B:H.73, B:H.108 HEM.7: 17 residues within 4Å: Chain C: M.53, F.54, F.56, H.73, V.77, M.80, R.103, L.104, T.107, H.108, Y.111, V.113, H.117, F.118, T.121, Y.150, L.153 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:M.53, C:F.54, C:F.54, C:V.77, C:L.104, C:Y.111, C:Y.111, C:V.113, C:F.118, C:F.118, C:Y.150, C:L.153, C:L.153 Salt bridges: C:K.69, C:R.103 pi-Stacking: C:H.108 Metal complexes: C:H.73, C:H.108 HEM.10: 20 residues within 4Å: Chain D: M.53, F.54, K.69, H.73, S.76, V.77, M.80, R.103, L.104, T.107, H.108, Y.111, V.113, H.117, F.118, T.121, Y.150, L.153, V.154, I.157 22 PLIP interactions: 22 interactions with chain D, Hydrophobic interactions: D:F.54, D:F.54, D:V.77, D:L.104, D:Y.111, D:Y.111, D:V.113, D:V.113, D:H.117, D:F.118, D:F.118, D:Y.150, D:L.153, D:L.153, D:V.154, D:I.157 Hydrogen bonds: D:T.107 Salt bridges: D:R.103 pi-Stacking: D:H.73 pi-Cation interactions: D:H.73 Metal complexes: D:H.73, D:H.108

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain B: R.110, Y.111 Chain C: K.162, P.163, D.164 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.164, C:D.164 Salt bridges: B:R.110 SO4.5: 5 residues within 4Å: Chain B: K.162, P.163, D.164 Chain C: R.110, Y.111 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:K.162, B:D.164, C:Y.111 Salt bridges: B:K.102, C:R.110 SO4.6: 3 residues within 4Å: Chain C: K.130, W.138, K.143 6 PLIP interactions: 6 interactions with chain C Water bridges: C:E.127, C:E.127, C:K.130, C:K.143 Salt bridges: C:K.130, C:K.143 SO4.8: 5 residues within 4Å: Chain A: R.110, Y.111 Chain D: K.162, P.163, D.164 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.162, D:D.164 Water bridges: D:K.102 Salt bridges: A:R.110 SO4.9: 5 residues within 4Å: Chain A: K.162, P.163, D.164 Chain D: R.110, Y.111 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.111, A:D.164 Salt bridges: D:R.110

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 7 residues within 4Å: Chain B: F.39, F.40, V.43, H.73, A.74, V.77, T.121 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.39, B:F.40, B:V.43 Salt bridges: B:H.73 ACY.11: 6 residues within 4Å: Chain D: F.39, F.40, H.73, A.74, V.77, T.121 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.39, D:F.40 Salt bridges: D:H.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smagghe, B.J. et al., The crystal structure of nonsymbiotic corn hemoglobin 1. To be Published

Release Date

2007-09-18

Peptides

Non-symbiotic hemoglobin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Non-symbiotic hemoglobin

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